Advertisement
Protein Structure and Folding| Volume 294, ISSUE 4, P1250-1256, January 25, 2019

Crystal structure of the complex between venom toxin and serum inhibitor from Viperidae snake

Open AccessPublished:November 30, 2018DOI:https://doi.org/10.1074/jbc.RA118.006840
      Venomous snakes have endogenous proteins that neutralize the toxicity of their venom components. We previously identified five small serum proteins (SSP-1–SSP-5) from a highly venomous snake belonging to the family Viperidae as inhibitors of various toxins from snake venom. The endogenous inhibitors belong to the prostate secretory protein of 94 amino acids (PSP94) family. SSP-2 interacts with triflin, which is a member of the cysteine-rich secretory protein (CRISP) family that blocks smooth muscle contraction. However, the structural basis for the interaction and the biological roles of these inhibitors are largely unknown. Here, we determined the crystal structure of the SSP-2–triflin complex at 2.3 Å resolution. A concave region centrally located in the N-terminal domain of triflin is fully occupied by the terminal β-strands of SSP-2. SSP-2 does not bind tightly to the C-terminal cysteine-rich domain of triflin; this domain is thought to be responsible for its channel-blocker function. Instead, the cysteine-rich domain is tilted 7.7° upon binding to SSP-2, and the inhibitor appears to sterically hinder triflin binding to calcium channels. These results help explain how an endogenous inhibitor prevents the venomous protein from maintaining homeostasis in the host. Furthermore, this interaction also sheds light on the binding interface between the human homologues PSP94 and CRISP-3, which are up-regulated in prostate and ovarian cancers.

      Introduction

      Venomous snakes pose a serious threat to public health, with at least 100,000 fatal cases of snake bites, as reported by the World Health Organization (WHO) each year (
      • Kasturiratne A.
      • Wickremasinghe A.
      • de Silva N.
      • Gunawardena N.
      • Pathmeswaran A.
      • Premaratna R.
      • Savioli L.
      • Lalloo D.
      • de Silva H.
      The global burden of snakebite: A literature analysis and modelling based on regional estimates of envenoming and deaths.
      ). Recent transcriptomic and proteomic studies have identified multiple components of Viperidae venoms, including cysteine-rich secretory proteins (CRISPs), metalloproteases, phospholipase A2, serine proteases, and C-type lectins. CRISP family proteins inhibit the function of membrane channels, but this inhibition activity itself is not sufficient to lead to death. The overall structure of CRISP family proteins is well-conserved (
      • Yamazaki Y.
      • Morita T.
      Structure and function of snake venom cysteine-rich secretory proteins.
      ) and has an N-terminal pathogenesis-related protein-1 (PR-1) domain, and a conserved divalent metal-ion–binding site is connected to a C-terminal cysteine-rich (CR)
      The abbreviations used are: CR
      cysteine-rich
      SSP
      small serum protein.
      domain by a hinge region (
      • Suzuki N.
      • Yamazaki Y.
      • Brown R.
      • Fujimoto Z.
      • Morita T.
      • Mizuno H.
      Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: Implications for movement of the C-terminal cysteine-rich domain.
      ,
      • Shikamoto Y.
      • Suto K.
      • Yamazaki Y.
      • Morita T.
      • Mizuno H.
      Crystal structure of a CRISP family Ca2+-channel blocker derived from snake venom.
      ). The CR domain and hinge linker are responsible for the channel-blocking function (
      • Zhou Q.
      • Wang Q.L.
      • Meng X.
      • Shu Y.
      • Jiang T.
      • Wagenknecht T.
      • Yin C.C.
      • Sui S.F.
      • Liu Z.
      Structural and functional characterization of ryanodine receptor-natrin toxin interaction.
      ).
      In contrast, venomous snakes possess three groups of endogenous antivenom components, which are found in snake serum as follows: (a) an antihemorrhagic factor (habu serum factor, HSF) that inhibits snake venom metalloproteases (
      • Yamakawa Y.
      • Omori-Satoh T.
      Primary structure of the antihemorrhagic factor in serum of the Japanese habu: A snake-venom metalloproteinase inhibitor with a double-headed cyctatin domain.
      ,
      • Deshimaru M.
      • Tanaka C.
      • Fujino K.
      • Aoki N.
      • Terada S.
      • Hattori S.
      • Ohno M.
      Properties and cDNA cloning of an antihemorrhagic factor (HSF) purified from the serum of Trimeresurus flavoviridis.
      ), (b) the phospholipase A2 inhibitors (
      • Dunn R.D.
      • Broady K.W.
      Snake inhibitors of phospholipase A2 enzymes.
      ), and (c) the small serum proteins (SSPs; SSP-1–SSP-5) previously discovered by us, which bind directly to toxic components (
      • Aoki N.
      • Sakiyama A.
      • Deshimaru M.
      • Terada S.
      Identification of novel serum proteins in a Japanese viper: Homologs of mammalian PSP94.
      ,
      • Aoki N.
      • Matsuo H.
      • Deshimaru M.
      • Terada S.
      Accelerated evolution of small serum proteins (SSPs)—The PSP94 family proteins in a Japanese viper.
      • Shioi N.
      • Deshimaru M.
      • Terada S.
      Structural analysis and characterization of new small serum proteins from the serum of a venomous snake (Gloydius blomhoffii).
      ). Interestingly, we found that each SSP targets different toxins. For example, SSP-1 targets the apoptosis-inducing venomous metalloprotease HV1 (
      • Masuda S.
      • Hayashi H.
      • Atoda H.
      • Morita T.
      • Araki S.
      Purification, cDNA cloning and characterization of the vascular apoptosis-inducing protein, HV1, from Trimeresurus flavoviridis.
      ), whereas SSP-3 targets the other metalloprotease, flavorase (
      • Shioi N.
      • Nishijima A.
      • Terada S.
      Flavorase, a novel non-haemorrhagic metalloproteinase in Protobothrops flavoviridis venom, is a target molecule of small serum protein-3.
      ). SSP-2 shows high affinity for triflin (
      • Aoki N.
      • Sakiyama A.
      • Kuroki K.
      • Maenaka K.
      • Kohda D.
      • Deshimaru M.
      • Terada S.
      Serotriflin, a CRISP family protein with binding affinity for small serum protein-2 in snake serum.
      ), a CRISP from habu snake venom that blocks Ca2+-channel activity. SSPs and triflin have human homologues: The prostate secretory protein of 94 amino acids (PSP94) and CRISP-3, respectively (
      • Yamazaki Y.
      • Morita T.
      Structure and function of snake venom cysteine-rich secretory proteins.
      ,
      • Aoki N.
      • Matsuo H.
      • Deshimaru M.
      • Terada S.
      Accelerated evolution of small serum proteins (SSPs)—The PSP94 family proteins in a Japanese viper.
      ). However, these endogenous antivenom groups remain unclear because of the lack of information on the three-dimensional structures of toxin and inhibitor complexes.
      PSP94, also known as β-microseminoprotein, is one of the most abundant proteins in the human seminal plasma, and its expression increases in prostate and ovarian cancer patients (
      • Whitaker H.C.
      • Warren A.Y.
      • Eeles R.
      • Kote-Jarai Z.
      • Neal D.E.
      The potential value of microseminoprotein-β as a prostate cancer biomarker and therapeutic target.
      ,
      • Ma J.
      • Yan B.
      • Zhang J.
      • Jiang B.
      • Guo Y.
      • Riedel H.
      • Mueller M.
      • Remick S.
      • Yu J.
      PSP94, an upstream signaling mediator of prostasin found highly elevated in ovarian cancer.
      ). In addition, CRISP-3 exists widely but is highly expressed in the prostate, salivary gland, epididymis, and ovary (
      • Krätzschmar J.
      • Haendler B.
      • Eberspaecher U.
      • Roosterman D.
      • Donner P.
      • Schleuning W.D.
      The human cysteine-rich secretory protein (CRISP) family primary structure and tissue distribution of CRISP-1, CRISP-2 and CRISP-3.
      ). Its expression is up-regulated in prostate cancer (
      • Asmann Y.W.
      • Kosari F.
      • Wang K.
      • Cheville J.C.
      • Vasmatzis G.
      Identification of differentially expressed genes in normal and malignant prostate by electronic profiling of expressed sequence tags.
      ) but reduced in patients with endometriosis (
      • Grande G.
      • Vincenzoni F.
      • Milardi D.
      • Pompa G.
      • Ricciardi D.
      • Fruscella E.
      • Mancini F.
      • Pontecorvi A.
      • Castagnola M.
      • Marana R.
      Cervical mucus proteome in endometriosis.
      ). Therefore, PSP94 and CRISP-3 have been attractive as potential drug targets and biomarkers for these diseases. The interaction between human PSP94 and CRISP was analyzed by NMR and binding studies (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ,
      • Breed A.
      • Gomes A.
      • Roy B.
      • Mahale S.
      • Pathak B.
      Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.
      ), and together with the PSP94 homodimer structure (
      • Kumar A.
      • Jagtap D.D.
      • Mahale S.D.
      • Kumar M.
      Crystal structure of prostate secretory protein P5P94 shows an edge-to-edge association of two monomers to form a homodimer.
      ), the CRISP-3–binding interface of PSP94 molecule was identified, proposing two distinct PSP94-CRISP complex models. Therefore, the PSP94–CRISP interactions are still largely ambiguous.
      Here, we show the first complex structure of PSP94 and CRISP family proteins, which explains the structural basis of SSP-2–mediated inhibition of triflin activity. Moreover, the triflin–SSP-2 complex structure enables us to provide a structural model of the PSP94–CRISP-3 complex.

      Results

      Overall crystal structure of the SSP-2–triflin complex

      SSP-2 effectively restores the toxic activity of triflin, which is mediated by the strong SSP-2–triflin binding (KD = 24 nm), as reported previously (
      • Aoki N.
      • Sakiyama A.
      • Kuroki K.
      • Maenaka K.
      • Kohda D.
      • Deshimaru M.
      • Terada S.
      Serotriflin, a CRISP family protein with binding affinity for small serum protein-2 in snake serum.
      ). However, the molecular basis of the SSP-2–triflin interaction is largely unknown. We determined the crystal structure of the SSP-2–triflin complex at 2.3 Å resolution using native proteins derived from snake serum and venom; these proteins possess many disulfide bonds and are difficult to produce in sufficient amounts from typical recombinant expression systems (Fig. 1 and Table S1). To the best of our knowledge, this is the first three-dimensional structure of a complex between a snake toxin and its endogenous inhibitor protein. The structure revealed that the SSP-2 N-terminal β1 strand (Ala1–Gly5) and partial C-terminal region (Leu59–Glu61), which are located on the same side of the molecule, insert into the central concave surface of the PR-1 domain of triflin. Approximately one fifth of the SSP-2 molecule is buried in the large cleft of the triflin molecule (1172.1 Å2; Fig. S1A, yellow region), which is smaller than the standard buried surface areas of protein-protein interactions (∼1600 Å2). However, this association is mediated by tight hydrogen bonding and electrostatic complementation (Fig. S1B and Table S2); this association is because of (i) 16 hydrogen bonds, including 6 interchain backbone hydrogen bonds, which is more than the average (
      • Lo Conte L.
      • Chothia C.
      • Janin J.
      The atomic structure of protein-protein recognition sites.
      ) and (ii) the complexation significance score calculated by the PISA software (
      • Krissinel E.
      • Henrick K.
      Inference of macromolecular assemblies from crystalline state.
      ), which ranges from 0 to 1 as interface relevance to complex formation increases, was 0.897, indicating a stable complex. Therefore, the interaction between SSP-2 and triflin was strong and in the nanomolar range, even though the interface was not large.
      Figure thumbnail gr1
      Figure 1Crystal structure of the SSP-2–triflin complex. A, cartoon representation of the SSP-2–triflin complex structure (left). SSP-2 is shown in orange; triflin is shown in pale green. The β-strands involved in the interaction are highlighted in red for SSP-2 (β1 and β5) and in dark green for triflin (β4). Disulfide bonds that are conserved among PSP94 family proteins are represented with sticks. The sulfur atoms are indicated in yellow. The disordered regions of SSP-2 (Ser10–Pro17) and triflin (Gln197–Asn204) in the crystal structure are indicated with a dotted line. The surface representation of the SSP-2–triflin complex is shown (top right). The left model is the same view as the cartoon representation on the left, whereas the right model represents a view rotated by 90° around a vertical axis. The enlarged view (bottom right) shows the 2FoFc electron density map of SSP-2 contoured at 2.0 σ (sky blue) at the interface with triflin. The structure of the complex shows that β5 (Leu59–Glu61) of SSP-2 forms a parallel β-sheet structure with β4 of triflin to interact with the toxin. B, sequence alignment of SSP-1 to SSP-5 from P. flavoviridis and the PSP94 family protein human PSP94. Universal Protein Resource (UniProt) accession numbers are as follows: A7VN13 (SSP-1), A7VN14 (SSP-2), A7VN15 (SSP-3), A7VN16 (SSP-4), and A7VN17 (SSP-5) from P. flavoviridis; P08118 (PSP94) from Homo sapiens. Highly conserved residues are shown in white font on a red background, and other conserved residues are shown in red font. Cysteine residues forming disulfide bridges are indicated below the alignment with a light green number. The same number indicates the paired residues for the disulfide bond. The secondary structures of SSP-2 and PSP94 obtained from the SSP-2–triflin complex and the PSP94 crystal structure (
      • Kumar A.
      • Jagtap D.D.
      • Mahale S.D.
      • Kumar M.
      Crystal structure of prostate secretory protein P5P94 shows an edge-to-edge association of two monomers to form a homodimer.
      ) are shown above and below the alignment, respectively. Black arrow indicates β-strand. T indicates a β-turn. The alignment figure was generated using Esprit (
      • Gouet P.
      • Robert X.
      • Courcelle E.
      ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.
      ). The residues whose side chains are involved in the interaction between SSP-2 and triflin are indicated with double circles. The residue numbers used throughout the manuscript are derived from this sequence alignment. Missing indicates a disordered region. The box with dashed lines indicates the β-strands that form an interchain β-sheet with triflin. The residues involved in the interaction with CRISP identified by the NMR experiment (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ) are indicated with diamonds below the alignment. Natural variants of PSP94 are also indicated with a yellow box. C, cartoon representation of the SSP-2 structure in the SSP-2–triflin complex. The orientation of SSP-2 is a view rotated 180° around a vertical axis, as shown in A. Conserved disulfide bonds are shown as ball and stick models with residue numbers in purple. See also and .

      Details of binding interfaces

      The N-terminal SSP-2 β1 strand interacts with His60, Lys72, His115, Asn152, Ile153, and Ile154 in the cleft of the triflin PR-1 domain (Fig. 2A and Fig. S2, A and D). In the unbound triflin (PDB ID: 1WVR) (
      • Shikamoto Y.
      • Suto K.
      • Yamazaki Y.
      • Morita T.
      • Mizuno H.
      Crystal structure of a CRISP family Ca2+-channel blocker derived from snake venom.
      ), a Cd2+ ion is coordinated by His60 and His115; this feature is well-conserved among CRISP family proteins (Fig. S3). The N-terminal Ala1 of SSP-2 is positioned at this site in the complex (Fig. 2A and Fig. S2E) and inhibits metal-binding activity. Furthermore, β1 and the neighboring β4 strand of SSP-2 interact with the triflin PR-1 domain via hydrophobic interactions and a β-sheet–like structure (Fig. 2A and Fig. S2). Glu44, Asp46, and Asp48 at the loop and β4 strand of SSP-2 comprise a negatively charged cluster and form salt bridges with Arg63 and Lys72 of triflin (Fig. 2B). This interaction is further enhanced by polar interactions between Ser51 Oγ of SSP-2 and Arg63 NΕ of triflin (
      • Kasturiratne A.
      • Wickremasinghe A.
      • de Silva N.
      • Gunawardena N.
      • Pathmeswaran A.
      • Premaratna R.
      • Savioli L.
      • Lalloo D.
      • de Silva H.
      The global burden of snakebite: A literature analysis and modelling based on regional estimates of envenoming and deaths.
      ) as well as Glu44 OΕ2 of SSP-2 and Arg63 main chain nitrogen atom of triflin (
      • Yamazaki Y.
      • Morita T.
      Structure and function of snake venom cysteine-rich secretory proteins.
      ) (Fig. 2B and Table S2). The entire SSP-2 C-terminal β5 strand and part of the β4 strand (Ile77–Ala80) of triflin form a parallel β-sheet via intermolecular hydrogen bonds (Fig. 2, C and D). The key amino acid residues that mediate this hydrophobic interaction are Tyr56, Leu59, and Leu69 of SSP-2 and Trp93, Val112, and His115 of triflin (Fig. 2C and Fig. S2B). Additional interactions were observed between the ethylene region of SSP-2 Glu61 and triflin Tyr78 and Thr81 (Fig. 2, C and D). In the triflin structure (PDB ID: 1WVR), Lys138 and Tyr139 form a typical cation-π interaction to stabilize this region of triflin, and the interaction is conserved in the complex form (Fig. 2D and Fig. S2F). Moreover, hydrogen bonding between SSP-2 Arg62 Nη1 and triflin Lys138 main chain oxygen atom, SSP-2 Ala63 main chain nitrogen atom and triflin Thr81 Oγ1 enhances the interaction in this region (Fig. 2D and Table S2). In summary, the β1 and β5 strands of SSP-2 comprise the horizontal long edge of the β-sheets that play central roles in the formation of the edge-to-edge binding interface that inhibits triflin function.
      Figure thumbnail gr2
      Figure 2Binding interface between SSP-2 and triflin. SSP-2 is shown as a cartoon model, whereas triflin is shown as a surface model. The complex structure is the same view as in the top right panel of A, showing the binding mode of SSP-2 in the cleft of triflin. A–D, the boxed regions are shown as detailed views. A, focused view of the β1 strand of SSP-2. Black dotted lines indicate hydrogen bonds. B, detailed view of the charge-charge interactions. The ion pair and hydrogen bonds are indicated with black dotted lines. A weak ion pair (>4.0 Å distance) between Asp48 of SSP-2 and Lys72 of triflin is also shown. C, detailed view of the C-terminal β-sheet formed by the SSP-2 β5 strand and the triflin β4 strand. Black dotted lines indicate hydrogen bonds, and related residues are shown as the stick model. The residues involved in the hydrophobic interaction are also indicated with the stick model. D, detailed view of the cation-π interaction between Lys138 and Tyr139 of triflin. Black dotted lines indicate hydrogen bonds. See also and .

      Structural basis for the binding specificity of SSPs

      Our previous report showed that among the five SSPs, only SSP-2 and SSP-5 could interact with triflin (
      • Aoki N.
      • Sakiyama A.
      • Kuroki K.
      • Maenaka K.
      • Kohda D.
      • Deshimaru M.
      • Terada S.
      Serotriflin, a CRISP family protein with binding affinity for small serum protein-2 in snake serum.
      ). The SSP-2–triflin complex structure shows that both the N- and C-terminal domains of SSP-2 are required for the interaction with triflin. SSP-3 and SSP-4 lack the C-terminal domain (Fig. 1B), which likely results in their failure to interact with triflin. In addition, the N terminus of the SSP-2 β5 strand is located deep inside the cavity of triflin, and the smaller amino acids Gly57 and Gly58 of SSP-2 and SSP-5 are surrounded by bulky residues, such as Ile77 and His115 (Fig. 2A and Fig. S2B). The presence of Asp55 in SSP-1 may cause steric hindrance that prevents the interaction with triflin. These structural features would therefore ensure the specificity of SSP family members.

      Discussion

      We demonstrated previously that a new class of endogenous inhibitors isolated from Japanese viper serum is capable of neutralizing distinct classes of snake toxin (
      • Aoki N.
      • Sakiyama A.
      • Deshimaru M.
      • Terada S.
      Identification of novel serum proteins in a Japanese viper: Homologs of mammalian PSP94.
      ,
      • Aoki N.
      • Matsuo H.
      • Deshimaru M.
      • Terada S.
      Accelerated evolution of small serum proteins (SSPs)—The PSP94 family proteins in a Japanese viper.
      • Shioi N.
      • Deshimaru M.
      • Terada S.
      Structural analysis and characterization of new small serum proteins from the serum of a venomous snake (Gloydius blomhoffii).
      ). Structural information of these toxin and inhibitor complexes would help in understanding the specificity and selectivity of the endogenous inhibitors.

      SSP-2–meditated inhibition of triflin activity

      Several ion channel targets of venom CRISPs from Viperidae and Elapidae have been identified and characterized (
      • Yamazaki Y.
      • Morita T.
      Structure and function of snake venom cysteine-rich secretory proteins.
      ). It is believed that the C-terminal CR domain of venom CRISPs is important for target molecule recognition (
      • Suzuki N.
      • Yamazaki Y.
      • Brown R.
      • Fujimoto Z.
      • Morita T.
      • Mizuno H.
      Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: Implications for movement of the C-terminal cysteine-rich domain.
      ,
      • Shikamoto Y.
      • Suto K.
      • Yamazaki Y.
      • Morita T.
      • Mizuno H.
      Crystal structure of a CRISP family Ca2+-channel blocker derived from snake venom.
      ) because the CR domain shares a conserved motif with ion channel blockers from sea anemones and scorpions (
      • Suzuki N.
      • Yamazaki Y.
      • Brown R.
      • Fujimoto Z.
      • Morita T.
      • Mizuno H.
      Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: Implications for movement of the C-terminal cysteine-rich domain.
      ,
      • Shikamoto Y.
      • Suto K.
      • Yamazaki Y.
      • Morita T.
      • Mizuno H.
      Crystal structure of a CRISP family Ca2+-channel blocker derived from snake venom.
      ,
      • Guo M.
      • Teng M.
      • Niu L.
      • Liu Q.
      • Huang Q.
      • Hao Q.
      Crystal structure of the cysteine-rich secretory protein stecrisp reveals that the cysteine-rich domain has a K+ channel inhibitor-like fold.
      ). In addition, a cryo-EM study showed that the hinge region (161–182) and CR domain (183–221) of natrin, a snake venom CRISP, are crucial for binding to the Ca2+ release channel ryanodine receptor 1 (
      • Zhou Q.
      • Wang Q.L.
      • Meng X.
      • Shu Y.
      • Jiang T.
      • Wagenknecht T.
      • Yin C.C.
      • Sui S.F.
      • Liu Z.
      Structural and functional characterization of ryanodine receptor-natrin toxin interaction.
      ). Our structure indicates that the CR domain of triflin exhibits few direct interactions with SSP-2 (Fig. 1A and Fig. S2C); however, upon binding, there is a conformational change. The superposition of free and SSP-2–bound forms of triflin shows that the CR domain is tilted by 7.7° toward SSP-2 (Fig. S4). SSP-2 is likely located sufficiently close to the triflin CR domain, raising the possibility to sterically hinder the interaction with an ion channel.

      Structural model for the PSP94-CRISP complex

      Over the last decade, researchers have awaited the identification of the interacting regions between PSP94 and a CRISP in mammals (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ,
      • Breed A.
      • Gomes A.
      • Roy B.
      • Mahale S.
      • Pathak B.
      Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.
      • Kumar A.
      • Jagtap D.D.
      • Mahale S.D.
      • Kumar M.
      Crystal structure of prostate secretory protein P5P94 shows an edge-to-edge association of two monomers to form a homodimer.
      ) in the context of the physiological relevance. In the present study, we determined the first structure of a PSP94-family protein in complex with a CRISP-family protein. PSP94 interacts strongly with triflin (
      • Hansson K.
      • Kjellberg M.
      • Fernlund P.
      Cysteine-rich secretory proteins in snake venoms form high affinity complexes with human and porcine β-microseminoproteins.
      ), and the terminal β1 and β8 strands of PSP94 are suggested to be involved in complex formation with CRISPs. Because SSP-2 has a significant structural similarity with PSP94, especially the N-terminal domain (Figs. 1C and 3, B–D), we superimposed PSP94 onto SSP-2 in our complex structure based on these facts to generate a hypothetical PSP94–CRISP–binding model (Fig. 3A). The key structural elements of the SSP-2 interface, such as the horizontal long edge of the β-sheet, are likely conserved in PSP94, aside from the β5 and β8 strands. This is because SSP-2 has a shorter C-terminal region than PSP94, and thus the N and C termini of SSP-2 are located on the opposite side of the molecule (Fig. 3, B and C). In our complex model, the β8 strand at the extended C-terminal of PSP94 likely plays the corresponding role of the β5 strand of SSP-2 in forming the binding surface (Fig. 3A). The alignment of venom CRISPs and human CRISP-3 showed that the important side chains for the interaction found in our complex are relatively well-conserved among CRISPs (Fig. S3), potentially explaining the ability of PSP94 to bind to a wide range of CRISPs (
      • Hansson K.
      • Kjellberg M.
      • Fernlund P.
      Cysteine-rich secretory proteins in snake venoms form high affinity complexes with human and porcine β-microseminoproteins.
      ). CRISP-interacting residues of PSP94 identified in earlier studies (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ,
      • Breed A.
      • Gomes A.
      • Roy B.
      • Mahale S.
      • Pathak B.
      Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.
      ) distribute similarly to triflin-interacting residues of SSP-2 (Fig. 3, B–D), indicating the conservation of the interface between PSP94- and CRISP-family proteins (Fig. 3A). Mapping of these residues on the structures also suggests the relevance of the conserved interaction (Fig. S5A). Although these data determined the binding interface, distinct complex models in the context of the orientation of PSP94 relative to CRISP have been proposed (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ,
      • Breed A.
      • Gomes A.
      • Roy B.
      • Mahale S.
      • Pathak B.
      Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.
      • Kumar A.
      • Jagtap D.D.
      • Mahale S.D.
      • Kumar M.
      Crystal structure of prostate secretory protein P5P94 shows an edge-to-edge association of two monomers to form a homodimer.
      ). Kumar et al. (
      • Kumar A.
      • Jagtap D.D.
      • Mahale S.D.
      • Kumar M.
      Crystal structure of prostate secretory protein P5P94 shows an edge-to-edge association of two monomers to form a homodimer.
      ) determined that the model of PSP94 binds to CRISP-3 in an antiparallel manner, which is the same orientation as our model, and is based on the crystal structure of the antiparallel PSP94 dimer. In contrast, Ghasriani et al. (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ) proposed a complex model in a parallel orientation using the NMR structure of PSP94. However, the orientation of the N-terminal domain relative to its C-terminal domain of PSP94 forms a straight face and is different from the twisted orientation of the NMR structure of PSP94, which may be important for the formation of the binding interface (
      • Kumar A.
      • Jagtap D.D.
      • Mahale S.D.
      • Kumar M.
      Crystal structure of prostate secretory protein P5P94 shows an edge-to-edge association of two monomers to form a homodimer.
      ). Therefore, the complex proposed here might be the first feasible model of the PSP94-CRISP complexes, although there could be a possibility of a distinct orientation.
      Figure thumbnail gr3
      Figure 3PSP94–CRISP–binding model. A, the partial N-terminal structure of the PSP94 family protein human PSP94 (PDB ID 3IX0) is superimposed on the structure of SSP-2 in complex with triflin, as determined in this study. The color of each molecule is the same as in and . The enlarged view shows which β-strands align to form interaction surface. The PSP94–CRISP-3 model based on NMR titration experiments show that the N-terminal Greek key motif and C-terminal β8 strand of PSP94 interact with the N-terminal PR-1 domain and hinge region of CRISP-3, respectively, in a parallel manner (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ). In contrast, our structure shows an upside-down, anti-parallel orientation, although the same side of the PSP94-family protein interacts with the same concave surface of the CRISP protein (A). B, the triflin-interacting residues are mapped on the SSP-2 with the stick model in yellow. C, CRISP-interacting residues identified by the NMR titration experiment (
      • Ghasriani H.
      • Fernlund P.
      • Udby L.
      • Drakenberg T.
      A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
      ) are mapped on PSP94 (PDB ID: 3IX0) with the stick model in pink. D, CRISP-interacting residues identified by the coimmunoprecipitation experiment using alanine or deletion mutants (
      • Breed A.
      • Gomes A.
      • Roy B.
      • Mahale S.
      • Pathak B.
      Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.
      ) are mapped on PSP94 with the stick model in purple. Disrupting the disulfide bond between the N- and C-terminal domains of PSP94 alters the unusual domain orientation, which indirectly abolishes the CRISP-interacting activity. The binding interface is located on the same side of the PSP94-family protein molecule, mainly composed of β1, β4, and β5 (for SSP-2) or β8 (for PSP94). E, the natural variants reported on the UniProt database (http://www.uniprot.org/) are mapped on PSP94 with the stick model in yellow. (Please note that the JBC is not responsible for the long-term archiving and maintenance of this site or any other third party hosted site.) Two of the residues, I5M and D60A, are located within the CRISP-binding interface. It is of note that seven other SNPs are found at the opposite side of the CRISP-binding interface. See also .
      Moreover, most of the natural variants of PSP94 are found far from the CRISP-binding interface (Fig. 3E). In CRISP-3, a few natural variants are also found to be inequivalent to the binding sites with PSP94 protein (Fig. S5B). Overall, our model provides important structural insight into the PSP94–hCRISP-3 complex, which is involved in prostate cancer and has been a contested target for many years.

      Conclusion

      To date, most studies have focused on relatively abundant and stable venom components. However, endogenous inhibitor proteins were evolutionarily acquired by venomous snakes to protect themselves and have not been fully characterized. Although triflin itself is not a lethal toxin, related ion channel blockers such as natrin induce serious clinical effects. Here, we described the molecular basis of the interaction of CRISP family toxins with endogenous inhibitors in venomous snakes. Furthermore, because an effective snakebite therapeutic molecule has yet to be developed, the crystal structure of the endogenous inhibitor-toxin complex provides valuable information for the rational design and development of antivenom drugs as well as the usefulness of SSPs as new therapeutic potentials. The structure also provides structural insight into the related PSP94-CRISP interactions involved in prostate and ovarian cancers.

      Experimental procedures

      Protein purification

      The serum and crude venom of P. flavoviridis were collected from snakes on Amami Island, Japan. SSP-2 was purified from the serum of P. flavoviridis as described previously (
      • Aoki N.
      • Sakiyama A.
      • Deshimaru M.
      • Terada S.
      Identification of novel serum proteins in a Japanese viper: Homologs of mammalian PSP94.
      ). Briefly, the serum was fractionated with cold ethanol, and the fraction containing SSPs was loaded onto two COSMOSIL 5C8-AR-300 columns (Nacalai Tesque, Kyoto, Japan); the first column was 20 × 150 mm, and the second column was 4.6 × 150 mm. Elution was carried out using a gradient of acetonitrile in 0.1% TFA at a flow rate of 5.0 or 1.0 ml per min, and absorbance was detected at 230 nm. Triflin was isolated from the crude venom of P. flavoviridis in three column chromatography steps as described previously (
      • Yamazaki Y.
      • Koike H.
      • Sugiyama Y.
      • Motoyoshi K.
      • Wada T.
      • Hishinuma S.
      • Mita M.
      • Morita T.
      Cloning and characterization of novel snake venom proteins that block smooth muscle contraction.
      ). The crude venom was fractionated on a Sephacryl S-300 HR column (5.0 × 90 cm; GE Healthcare) in 50 mm Tris-HCl buffer, pH 8.0, 50 mm NaCl, and 5 mm CaCl2. The third fraction containing triflin was injected onto the SP Sepharose Fast Flow column (5 ml; GE Healthcare) in 10 mm phosphate buffer (pH 6.8) and eluted with a linear gradient to 0.25 m NaCl. The obtained fractions were applied onto a HiLoad Superdex 75 column (1.6 × 60 cm, GE Healthcare) equilibrated with 20 mm Tris-HCl, pH 8.0, and 200 mm NaCl. The quality and quantity of the purified SSP-2 and triflin were assessed by SDS-PAGE and protein sequencer (Shimadzu, Kyoto, Japan), and the concentration of pure samples was determined using a spectrophotometer as described previously (
      • Aoki N.
      • Sakiyama A.
      • Deshimaru M.
      • Terada S.
      Identification of novel serum proteins in a Japanese viper: Homologs of mammalian PSP94.
      ).

      Crystallization of the SSP-2–triflin complex

      Both triflin and SSP-2 proteins were purified directly from P. flavoviridis venom or serum, as described above. These proteins possess eight and five disulfide bonds, respectively, and are difficult to produce in sufficient amounts from Escherichia coli, insect cells, or cell-free protein synthesis systems. To obtain the SSP-2–triflin complex, purified SSP-2 and triflin were mixed in a 1:1 molar ratio and incubated for 2 h at 4 °C. The protein mixture was subsequently applied to a Superdex 75 10/300 GL column (GE Healthcare) for purification. The fractions containing the protein complex were collected and concentrated to 4.8 mg/ml as determined by the Bradford protein assay method in 10 mm Tris-HCl, pH 8.0, containing 100 mm NaCl and 5 mm CaCl2 using a Millipore filter device (Amicon, Nihon Millipore, Tokyo, Japan). Screening for the crystallization was initially carried out using the ProPlex (Molecular Dimensions, Suffolk, UK) and Classics II (Qiagen, Germantown, Maryland) screening kits using the sitting-drop vapor-diffusion method. Drops were formed by mixing the SSP-2–triflin complex and reservoir solution in a 1:1 ratio (0.05 μl each) using a Mosquito robot (TTP Labtech, Melbourn, UK), and the crystals were grown at 20 °C. Native crystals of the SSP-2–triflin complex appeared under several conditions used in the commercial screening kits, and crystals suitable for X-ray diffraction analysis were obtained using ProPlex solution No. 2.12 (0.2 m ammonium sulfate, 0.1 m MES, pH 6.5, 20% (w/v) PEG 8000).

      Data collection and structure determination of the SSP-2–triflin complex

      X-ray diffraction data sets for the SSP-2–triflin complex crystal were collected at 100 K using synchrotron radiation at the BL44XU station at SPring-8, Harima, Hyogo, Japan and processed using the HKL2000 program (
      • Otwinowski Z.
      • Minor W.
      Processing of X-ray diffraction data collected in oscillation mode.
      ). X-ray diffraction experiments showed that crystals of the SSP-2–triflin complex belong to the C2 space group with the following unit cell parameters: a = 111.2 Å, b = 48.1 Å, c = 75.0 Å, α = γ = 90°, and β = 103°. The structure was solved using the molecular replacement method and the program MOLREP (
      • Vagin A.
      • Teplyakov A.
      MOLREP: An automated program for molecular replacement.
      ). The crystal structures of triflin (PDB ID: 1WVR) and PSP94 (PDB ID: 3IX0) were used as search models. Automatic model building was carried out using ARP/wARP (
      • Langer G.
      • Cohen S.X.
      • Lamzin V.S.
      • Perrakis A.
      Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.
      ). Model modification and structure refinement were performed using COOT (
      • Emsley P.
      • Cowtan K.
      Coot: Model-building tools for molecular graphics.
      ), REFMAC5 (
      • Murshudov G.
      • Vagin A.
      • Dodson E.
      Refinement of macromolecular structures by the maximum-likelihood method.
      ), and PHENIX (
      • Adams P.
      • Afonine P.
      • Bunkoczi G.
      • Chen V.
      • Davis I.
      • Echols N.
      • Headd J.
      • Hung L.
      • Kapral G.
      • Grosse-Kunstleve R.
      • McCoy A.
      • Moriarty N.
      • Oeffner R.
      • Read R.
      • Richardson D.
      • Richardson J.
      • Terwilliger T.
      • Zwart P.
      PHENIX: A comprehensive Python-based system for macromolecular structure solution.
      ). The quality of the final model was validated using the MolProbity program (
      • Chen V.
      • Arendall W.
      • Headd J.
      • Keedy D.
      • Immormino R.
      • Kapral G.
      • Murray L.
      • Richardson J.
      • Richardson D.
      MolProbity: All-atom structure validation for macromolecular crystallography.
      ). The final structure was refined to an R factor of 18.6% and Rfree of 21.9% up to a 2.3 Å resolution, as summarized in Table S1. We were unable to build a model of the Pro11-Met15 region of SSP-2, located on the opposite side of the binding interface to triflin, because of poor electron density. The coordinates for the refined SSP-2–triflin complex structure have been deposited in the Protein Data Bank (PDB ID: 6IMF). Figures depicting the protein structure were generated using PyMOL.

      Accession code

      The atomic coordinates and structural factors for the SSP-2–triflin complex have been deposited in the RCSB Protein Data Bank under the accession code 6IMF.

      Author contributions

      N. S., S. T., and K. M. conceptualization; N. S., Y. O., H. M., and K. M. resources; N. S., T. T., S. T., and K. M. supervision; N. S. and K. M. funding acquisition; N. S., T. T., S. S., Y. O., K. K., and K. M. investigation; N. S., T. T., S. S., and Y. O. writing-original draft; N. S., T. T., S. T., and K. M. project administration; N. S., T. T., and K. M. writing-review and editing; T. T., S. S., H. M., S. K., and T. O. formal analysis; T. T., S. K., T. O., and K. K. validation; T. T. visualization.

      Acknowledgments

      We thank Professor Takahito Chigiwa (So-jo University) for providing information about the venom components of P. flavoviridis]. We also thank Yaopeng Hu (Fukuoka University) and Lin Hai Kurahara (Fukuoka University) for the useful discussion. We are grateful to Professor R. Manjunatha KINI (National University Singapore) for helpful discussions. We thank the beamline staff of the Photon Factory and SPring-8 for their assistance with X-ray diffraction data collection.

      Supplementary Material

      References

        • Kasturiratne A.
        • Wickremasinghe A.
        • de Silva N.
        • Gunawardena N.
        • Pathmeswaran A.
        • Premaratna R.
        • Savioli L.
        • Lalloo D.
        • de Silva H.
        The global burden of snakebite: A literature analysis and modelling based on regional estimates of envenoming and deaths.
        PLoS Med. 2008; 5 (18986210): e218
        • Yamazaki Y.
        • Morita T.
        Structure and function of snake venom cysteine-rich secretory proteins.
        Toxicon. 2004; 44 (15302528): 227-231
        • Suzuki N.
        • Yamazaki Y.
        • Brown R.
        • Fujimoto Z.
        • Morita T.
        • Mizuno H.
        Structures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: Implications for movement of the C-terminal cysteine-rich domain.
        Acta Crystallogr. D Biol. Crystallogr. 2008; 64 (18931410): 1034-1042
        • Shikamoto Y.
        • Suto K.
        • Yamazaki Y.
        • Morita T.
        • Mizuno H.
        Crystal structure of a CRISP family Ca2+-channel blocker derived from snake venom.
        J. Mol. Biol. 2005; 350 (15953617): 735-743
        • Zhou Q.
        • Wang Q.L.
        • Meng X.
        • Shu Y.
        • Jiang T.
        • Wagenknecht T.
        • Yin C.C.
        • Sui S.F.
        • Liu Z.
        Structural and functional characterization of ryanodine receptor-natrin toxin interaction.
        Biophys. J. 2008; 95 (18658224): 4289-4299
        • Yamakawa Y.
        • Omori-Satoh T.
        Primary structure of the antihemorrhagic factor in serum of the Japanese habu: A snake-venom metalloproteinase inhibitor with a double-headed cyctatin domain.
        J. Biochem. 1992; 112 (1478916): 583-589
        • Deshimaru M.
        • Tanaka C.
        • Fujino K.
        • Aoki N.
        • Terada S.
        • Hattori S.
        • Ohno M.
        Properties and cDNA cloning of an antihemorrhagic factor (HSF) purified from the serum of Trimeresurus flavoviridis.
        Toxicon. 2005; 46 (16289179): 937-945
        • Dunn R.D.
        • Broady K.W.
        Snake inhibitors of phospholipase A2 enzymes.
        Biochim. Biophys. Acta. 2001; 1533 (11514233): 29-37
        • Aoki N.
        • Sakiyama A.
        • Deshimaru M.
        • Terada S.
        Identification of novel serum proteins in a Japanese viper: Homologs of mammalian PSP94.
        Biochem. Biophys. Res. Commun. 2007; 359 (17543280): 330-334
        • Aoki N.
        • Matsuo H.
        • Deshimaru M.
        • Terada S.
        Accelerated evolution of small serum proteins (SSPs)—The PSP94 family proteins in a Japanese viper.
        Gene. 2008; 426 (18817856): 7-14
        • Shioi N.
        • Deshimaru M.
        • Terada S.
        Structural analysis and characterization of new small serum proteins from the serum of a venomous snake (Gloydius blomhoffii).
        Biosci. Biotechnol. Biochem. 2014; 78 (25036827): 410-419
        • Masuda S.
        • Hayashi H.
        • Atoda H.
        • Morita T.
        • Araki S.
        Purification, cDNA cloning and characterization of the vascular apoptosis-inducing protein, HV1, from Trimeresurus flavoviridis.
        Eur. J. Biochem. 2001; 268 (11389737): 3339-3345
        • Shioi N.
        • Nishijima A.
        • Terada S.
        Flavorase, a novel non-haemorrhagic metalloproteinase in Protobothrops flavoviridis venom, is a target molecule of small serum protein-3.
        J. Biochem. 2015; 158 (25681613): 37-48
        • Aoki N.
        • Sakiyama A.
        • Kuroki K.
        • Maenaka K.
        • Kohda D.
        • Deshimaru M.
        • Terada S.
        Serotriflin, a CRISP family protein with binding affinity for small serum protein-2 in snake serum.
        Biochim. Biophys. Acta. 2008; 1784 (18222185): 621-628
        • Whitaker H.C.
        • Warren A.Y.
        • Eeles R.
        • Kote-Jarai Z.
        • Neal D.E.
        The potential value of microseminoprotein-β as a prostate cancer biomarker and therapeutic target.
        Prostate. 2010; 70 (19790236): 333-340
        • Ma J.
        • Yan B.
        • Zhang J.
        • Jiang B.
        • Guo Y.
        • Riedel H.
        • Mueller M.
        • Remick S.
        • Yu J.
        PSP94, an upstream signaling mediator of prostasin found highly elevated in ovarian cancer.
        Cell Death Dis. 2014; 5 (25188517): e1407
        • Krätzschmar J.
        • Haendler B.
        • Eberspaecher U.
        • Roosterman D.
        • Donner P.
        • Schleuning W.D.
        The human cysteine-rich secretory protein (CRISP) family primary structure and tissue distribution of CRISP-1, CRISP-2 and CRISP-3.
        Eur. J. Biochem. 1996; 236 (8665901): 827-836
        • Asmann Y.W.
        • Kosari F.
        • Wang K.
        • Cheville J.C.
        • Vasmatzis G.
        Identification of differentially expressed genes in normal and malignant prostate by electronic profiling of expressed sequence tags.
        Cancer Res. 2002; 62 (12036949): 3308-3314
        • Grande G.
        • Vincenzoni F.
        • Milardi D.
        • Pompa G.
        • Ricciardi D.
        • Fruscella E.
        • Mancini F.
        • Pontecorvi A.
        • Castagnola M.
        • Marana R.
        Cervical mucus proteome in endometriosis.
        Clin. Proteomics. 2017; 14 (28174513): 7
        • Ghasriani H.
        • Fernlund P.
        • Udby L.
        • Drakenberg T.
        A model of the complex between human β-microseminoprotein and CRISP-3 based on NMR data.
        Biochem. Biophys. Res. Commun. 2009; 378 (19026612): 235-239
        • Breed A.
        • Gomes A.
        • Roy B.
        • Mahale S.
        • Pathak B.
        Mapping of the binding sites involved in PSP94-CRISP-3 interaction by molecular dissection of the complex.
        Biochim. Biophys. Acta. 2013; 1830 (23375721): 3019-3029
        • Kumar A.
        • Jagtap D.D.
        • Mahale S.D.
        • Kumar M.
        Crystal structure of prostate secretory protein P5P94 shows an edge-to-edge association of two monomers to form a homodimer.
        J. Mol. Biol. 2010; 397 (20184897): 947-956
        • Lo Conte L.
        • Chothia C.
        • Janin J.
        The atomic structure of protein-protein recognition sites.
        J. Mol. Biol. 1999; 285 (9925793): 2177-2198
        • Krissinel E.
        • Henrick K.
        Inference of macromolecular assemblies from crystalline state.
        J. Mol. Biol. 2007; 372 (17681537): 774-797
        • Guo M.
        • Teng M.
        • Niu L.
        • Liu Q.
        • Huang Q.
        • Hao Q.
        Crystal structure of the cysteine-rich secretory protein stecrisp reveals that the cysteine-rich domain has a K+ channel inhibitor-like fold.
        J. Biol. Chem. 2005; 280 (15596436): 12405-12412
        • Hansson K.
        • Kjellberg M.
        • Fernlund P.
        Cysteine-rich secretory proteins in snake venoms form high affinity complexes with human and porcine β-microseminoproteins.
        Toxicon. 2009; 54 (19341830): 128-137
        • Yamazaki Y.
        • Koike H.
        • Sugiyama Y.
        • Motoyoshi K.
        • Wada T.
        • Hishinuma S.
        • Mita M.
        • Morita T.
        Cloning and characterization of novel snake venom proteins that block smooth muscle contraction.
        Eur. J. Biochem. 2002; 269 (12047379): 2708-2715
        • Otwinowski Z.
        • Minor W.
        Processing of X-ray diffraction data collected in oscillation mode.
        Methods Enzymol. 1997; 276 (27799103): 307-326
        • Vagin A.
        • Teplyakov A.
        MOLREP: An automated program for molecular replacement.
        J. Appl. Crystallogr. 1997; 30: 1022-1025
        • Langer G.
        • Cohen S.X.
        • Lamzin V.S.
        • Perrakis A.
        Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.
        Nat. Protoc. 2008; 3 (18600222): 1171-1179
        • Emsley P.
        • Cowtan K.
        Coot: Model-building tools for molecular graphics.
        Acta Crystallogr. D Biol. Crystallogr. 2004; 60 (15572765): 2126-2132
        • Murshudov G.
        • Vagin A.
        • Dodson E.
        Refinement of macromolecular structures by the maximum-likelihood method.
        Acta Crystallogr. D Biol. Crystallogr. 1997; 53 (15299926): 240-255
        • Adams P.
        • Afonine P.
        • Bunkoczi G.
        • Chen V.
        • Davis I.
        • Echols N.
        • Headd J.
        • Hung L.
        • Kapral G.
        • Grosse-Kunstleve R.
        • McCoy A.
        • Moriarty N.
        • Oeffner R.
        • Read R.
        • Richardson D.
        • Richardson J.
        • Terwilliger T.
        • Zwart P.
        PHENIX: A comprehensive Python-based system for macromolecular structure solution.
        Acta Crystallogr. D Biol. Crystallogr. 2010; 66 (20124702): 213-221
        • Chen V.
        • Arendall W.
        • Headd J.
        • Keedy D.
        • Immormino R.
        • Kapral G.
        • Murray L.
        • Richardson J.
        • Richardson D.
        MolProbity: All-atom structure validation for macromolecular crystallography.
        Acta Crystallogr. D Biol. Crystallogr. 2010; 66 (20057044): 12-21
        • Gouet P.
        • Robert X.
        • Courcelle E.
        ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins.
        Nucleic Acids Res. 2003; 31 (12824317): 3320-3323