4XMN

Structure of the yeast coat nucleoporin complex, space group P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.6 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.318 

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:  

  • 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 ...

    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. These authors contributed equally to this work.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein SEC13
A
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SEC13 (ANU3)
Find proteins for Q04491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SEC13
Go to UniProtKB:  Q04491
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP145
B
652Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NUP145 (RAT10)
EC: 3.4.21.-
Find proteins for P49687 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P49687
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP84
F
454Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NUP84
Find proteins for P52891 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P52891
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP120
E
1045Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NUP120 (RAT2)
Find proteins for P35729 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35729
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP85
D
685Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: NUP85 (RAT9)
Find proteins for P46673 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NUP85
Go to UniProtKB:  P46673
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Antibody 87 light chain
L
217N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Antibody 87 heavy chain
H
267N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, D, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.6 Å
  • R-Value Free: 0.347 
  • R-Value Work: 0.318 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.130α = 90.00
b = 179.950β = 90.00
c = 441.180γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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