2RFO

Crystral Structure of the nucleoporin Nic96


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of the nic96 subcomplex organization in the nuclear pore channel.

Schrader, N.Stelter, P.Flemming, D.Kunze, R.Hurt, E.Vetter, I.R.

(2008) Mol Cell 29: 46-55

  • DOI: 10.1016/j.molcel.2007.10.022
  • Primary Citation of Related Structures:  
    2RFO

  • PubMed Abstract: 
  • Nic96 is a conserved nucleoporin that recruits the Nsp1-Nup49-Nup57 complex, a module with Phe-Gly (FG) repeats, to the central transport channel of the nuclear pore complex (NPC). Nic96 binds the Nsp1 complex via its N domain and assembles into the NPC framework via its central and C domain ...

    Nic96 is a conserved nucleoporin that recruits the Nsp1-Nup49-Nup57 complex, a module with Phe-Gly (FG) repeats, to the central transport channel of the nuclear pore complex (NPC). Nic96 binds the Nsp1 complex via its N domain and assembles into the NPC framework via its central and C domain. Here, we report the crystal structure of a large structural nucleoporin, Nic96 without its N domain (Nic96DeltaN). Nic96DeltaN is composed of three domains and is a straight molecule that--although almost entirely helical--exhibits strong deviations from the predicted alpha-solenoid fold. The missing N domain projects midway from the Nic96 molecule, indicating how the Nsp1 complex might be located with respect to the rod-like Nic96. Notably, Nic96DeltaN binds in vitro to FG repeats of the Nsp1 complex. These data suggest a model of how Nic96 could organize a transport module with coiled-coil domains and FG repeats in the central pore channel.


    Organizational Affiliation

    Max-Planck-Institut für Molekulare Physiologie, Abteilung Strukturelle Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NIC96A, B651Saccharomyces 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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62α = 62
b = 100β = 82
c = 104γ = 86
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description