3JRO

NUP84-NUP145C-SEC13 edge element of the NPC lattice


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.286 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice.

Brohawn, S.G.Schwartz, T.U.

(2009) Nat Struct Mol Biol 16: 1173-1177

  • DOI: https://doi.org/10.1038/nsmb.1713
  • Primary Citation of Related Structures:  
    3JRO, 3JRP

  • PubMed Abstract: 

    Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport. These massive protein assemblies are modular, with a stable structural scaffold supporting more dynamically attached components. The scaffold is made from multiple copies of the heptameric Y complex and the heteromeric Nic96 complex. We previously showed that members of these core subcomplexes specifically share an ACE1 fold with Sec31 of the COPII vesicle coat, and we proposed a lattice model for the NPC based on this commonality. Here we present the crystal structure of the heterotrimeric 134-kDa complex of Nup84-Nup145C-Sec13 of the Y complex. The heterotypic ACE1 interaction of Nup84 and Nup145C is analogous to the homotypic ACE1 interaction of Sec31 that forms COPII lattice edge elements and is inconsistent with the alternative 'fence-like' NPC model. We construct a molecular model of the Y complex and compare the architectural principles of COPII and NPC lattices.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion Protein of Protein Transport Protein SEC13 and Nucleoporin NUP145753Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04491 
Go to UniProtKB:  Q04491
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49687 
Go to UniProtKB:  P49687
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ04491P49687
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP84B [auth C]426Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUP84YDL116W
UniProt
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P52891 
Go to UniProtKB:  P52891
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52891
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.286 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.472α = 90
b = 170.472β = 90
c = 270.732γ = 120
Software Package:
Software NamePurpose
ADSCdata 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: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-13
    Changes: Other
  • Version 1.3: 2017-08-02
    Changes: Refinement description, Source and taxonomy