4XMM

Structure of the yeast coat nucleoporin complex, space group C2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.38 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.330 
  • R-Value Observed: 0.332 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: SEC13, ANU3, YLR208W, L8167.4
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q04491
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP145B652Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP145, RAT10, YGL092W
EC: 3.4.21
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin SEH1C349Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEH1, YGL100W
Find proteins for P53011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP85D715Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP85, RAT9, YJR042W, J1624
Find proteins for P46673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP120E1045Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP120, RAT2, YKL057C, YKL313, YKL314
Find proteins for P35729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP84F454Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NUP84, YDL116W
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 57 heavy chainG [auth H]271Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Antibody 57 light chainH [auth L]217Homo sapiensMutation(s): 0 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.38 Å
  • R-Value Free: 0.353 
  • R-Value Work: 0.330 
  • R-Value Observed: 0.332 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.645α = 90
b = 186.297β = 100.85
c = 199.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 T32 GM07616
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU01 GM094588
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM087519

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: Database references
  • Version 1.3: 2016-07-20
    Changes: Data collection
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence