2QX5

Structure of nucleoporin Nic96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1074/jbc.M705479200

  • 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. Ho ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NIC96
A, B
661Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NIC96
Find proteins for P34077 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P34077
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 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 = 90.00
b = 82.478β = 91.11
c = 113.028γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance