3EWE

Crystal Structure of the Nup85/Seh1 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.326 
  • R-Value Observed: 0.328 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural evidence for common ancestry of the nuclear pore complex and vesicle coats.

Brohawn, S.G.Leksa, N.C.Spear, E.D.Rajashankar, K.R.Schwartz, T.U.

(2008) Science 322: 1369-1373

  • DOI: https://doi.org/10.1126/science.1165886
  • Primary Citation of Related Structures:  
    3EWE

  • PubMed Abstract: 

    Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.


  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin SEH1
A, C
349Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEH1YGL100W
UniProt
Find proteins for P53011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53011 
Go to UniProtKB:  P53011
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53011
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP85
B, D
564Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: J1624NUP85RAT9YJR042W
UniProt
Find proteins for P46673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46673 
Go to UniProtKB:  P46673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46673
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.326 
  • R-Value Observed: 0.328 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.559α = 90
b = 112.559β = 90
c = 350.549γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-09
    Changes: Structure summary