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J. Biol. Chem., Vol. 282, Issue 48, 34904-34912, November 30, 2007

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Crystal Structure of Nucleoporin Nic96 Reveals a Novel, Intricate Helical Domain Architecture^*

From the Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139

The nuclear pore complex (NPC) is an elaborate protein machine that mediates macromolecular transport across the nuclear envelope in all eukaryotes. The NPC is formed by nucleoporins that assemble in multiple copies around an 8-fold symmetry axis. Homology modeling suggests that most architectural nucleoporins are composed of simple β-propeller and -helical repeat domains. Here we present the crystal structure of Nic96, the Nup93 homolog in Saccharomyces cerevisiae, one of the major components of the NPC. This is the first structure of an -helical nucleoporin domain. The protein folds into an elongated, mostly -helical structure. Characteristically, non-canonical architectural features define the Nic96 structure. Sequence conservation among Nup93 homologs across all eukaryotes strongly suggests that the distinct topology is evolutionarily well maintained. We propose that the unique Nic96/Nup93 fold has a conserved function in all eukaryotes.

Received for publication, July 5, 2007 , and in revised form, September 21, 2007.

The atomic coordinates and structure factors (code 2QX5) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by National Institutes of Health Grant GM077537. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. 1 and 2.

¹ To whom correspondence should be addressed: Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. 68-480, Cambridge, MA 02139. Tel.: 617-452-3851; Fax: 617-258-6553; E-mail: tus{at}mit.edu.

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