3I4R

Nup107(aa658-925)/Nup133(aa517-1156) complex, H.sapiens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.320 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architectural nucleoporins Nup157/170 and Nup133 are structurally related and descend from a second ancestral element.

Whittle, J.R.Schwartz, T.U.

(2009) J Biol Chem 284: 28442-28452

  • DOI: https://doi.org/10.1074/jbc.M109.023580
  • Primary Citation of Related Structures:  
    3I4R, 3I5P, 3I5Q

  • PubMed Abstract: 

    The nuclear pore complex (NPC) constitutes one of the largest protein assemblies in the eukaryotic cell and forms the exclusive gateway to the nucleus. The stable, approximately 15-20-MDa scaffold ring of the NPC is built from two multiprotein complexes arranged around a central 8-fold axis. Here we present crystal structures of two large architectural units, yNup170(979-1502) and hNup107(658-925) x hNup133(517-1156), each a constituent of one of the two multiprotein complexes. Conservation of domain arrangement and of tertiary structure suggests that Nup157/170 and Nup133 derived from a common ancestor. Together with the previously established ancestral coatomer element (ACE1), these two elements constitute the major alpha-helical building blocks of the NPC scaffold and define its branched, lattice-like architecture, similar to vesicle coats like COPII. We hypothesize that the extant NPC evolved early during eukaryotic evolution from a rudimentary structure composed of several identical copies of a few ancestral elements, later diversified and specified by gene duplication.


  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup107277Homo sapiensMutation(s): 0 
Gene Names: NUP107
UniProt & NIH Common Fund Data Resources
Find proteins for P57740 (Homo sapiens)
Explore P57740 
Go to UniProtKB:  P57740
PHAROS:  P57740
GTEx:  ENSG00000111581 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57740
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear pore complex protein Nup133644Homo sapiensMutation(s): 0 
Gene Names: NUP133
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUM0 (Homo sapiens)
Explore Q8WUM0 
Go to UniProtKB:  Q8WUM0
PHAROS:  Q8WUM0
GTEx:  ENSG00000069248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUM0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.53 Å
  • R-Value Free: 0.370 
  • R-Value Work: 0.315 
  • R-Value Observed: 0.320 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.554α = 90
b = 133.047β = 90
c = 176.303γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references