2QX5

Structure of nucleoporin Nic96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture

Jeudy, S.Schwartz, T.U.

(2007) J Biol Chem 282: 34904

  • DOI: https://doi.org/10.1074/jbc.M705479200
  • Primary Citation of Related Structures:  
    2QX5

  • PubMed Abstract: 

    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 beta-propeller and alpha-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 alpha-helical nucleoporin domain. The protein folds into an elongated, mostly alpha-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.


  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NIC96
A, B
661Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NIC96
UniProt
Find proteins for P34077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P34077 
Go to UniProtKB:  P34077
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34077
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.121α = 90
b = 82.478β = 91.11
c = 113.028γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations