4XMN

Structure of the yeast coat nucleoporin complex, space group P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.60 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.321 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nuclear pores. Architecture of the nuclear pore complex coat.

Stuwe, T.Correia, A.R.Lin, D.H.Paduch, M.Lu, V.T.Kossiakoff, A.A.Hoelz, A.

(2015) Science 347: 1148-1152

  • DOI: 10.1126/science.aaa4136
  • Primary Citation of Related Structures:  
    4XMM, 4XMN

  • PubMed Abstract: 
  • The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7 ...

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7.4 angstrom resolution. The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central "triskelion" of the Y. A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture. Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully assembled human NPC, thereby accounting for ~16 megadalton of its mass.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA. hoelz@caltech.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein SEC13A297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEC13ANU3YLR208WL8167.4
UniProt
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q04491
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UniProt GroupQ04491
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP145B652Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP145RAT10YGL092W
EC: 3.4.21
UniProt
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP49687
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP84C [auth F]454Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP84YDL116W
UniProt
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP52891
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP120D [auth E]1,045Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP120RAT2YKL057CYKL313YKL314
UniProt
Find proteins for P35729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP35729
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP85E [auth D]685Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP85RAT9YJR042WJ1624
UniProt
Find proteins for P46673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP46673
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 87 light chainF [auth L]217synthetic constructMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 87 heavy chainG [auth H]267synthetic constructMutation(s): 0 
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Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.60 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.318 
  • R-Value Observed: 0.321 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.13α = 90
b = 179.95β = 90
c = 441.18γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Structure summary
  • Version 1.2: 2016-02-03
    Changes: Source and taxonomy