3F3G | pdb_00003f3g

Crystal structure of the nucleoporin pair Nup85-Seh1, space group P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 
    0.272 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

A fence-like coat for the nuclear pore membrane.

Debler, E.W.Ma, Y.Seo, H.S.Hsia, K.C.Noriega, T.R.Blobel, G.Hoelz, A.

(2008) Mol Cell 32: 815-826

  • DOI: https://doi.org/10.1016/j.molcel.2008.12.001
  • Primary Citation Related Structures: 
    3F3F, 3F3G, 3F3P

  • PubMed Abstract: 

    We recently proposed a cylindrical coat for the nuclear pore membrane in the nuclear pore complex (NPC). This scaffold is generated by multiple copies of seven nucleoporins. Here, we report three crystal structures of the nucleoporin pair Seh1*Nup85, which is part of the coat cylinder. The Seh1*Nup85 assembly bears resemblance in its shape and dimensions to that of another nucleoporin pair, Sec13*Nup145C. Furthermore, the Seh1*Nup85 structures reveal a hinge motion that may facilitate conformational changes in the NPC during import of integral membrane proteins and/or during nucleocytoplasmic transport. We propose that Seh1*Nup85 and Sec13*Nup145C form 16 alternating, vertical rods that are horizontally linked by the three remaining nucleoporins of the coat cylinder. Shared architectural and mechanistic principles with the COPII coat indicate a common evolutionary origin and support the notion that the NPC coat represents another class of membrane coats.


  • Organizational Affiliation
    • Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 417.34 kDa 
  • Atom Count: 25,114 
  • Modeled Residue Count: 3,147 
  • Deposited Residue Count: 3,684 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoporin SEH1
A, B, E, F
351Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SEH1
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoporin NUP85
C, D, G, H
570Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NUP85RAT9
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: 3.75 Å
  • R-Value Free:  0.272 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.377α = 90
b = 106.487β = 90
c = 358.636γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNSrefinement
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: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description