5CWS

Crystal structure of the intact Chaetomium thermophilum Nsp1-Nup49-Nup57 channel nucleoporin heterotrimer bound to its Nic96 nuclear pore complex attachment site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.77 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Architecture of the fungal nuclear pore inner ring complex.

Stuwe, T.Bley, C.J.Thierbach, K.Petrovic, S.Schilbach, S.Mayo, D.J.Perriches, T.Rundlet, E.J.Jeon, Y.E.Collins, L.N.Huber, F.M.Lin, D.H.Paduch, M.Koide, A.Lu, V.Fischer, J.Hurt, E.Koide, S.Kossiakoff, A.A.Hoelz, A.

(2015) Science 350: 56-64

  • DOI: https://doi.org/10.1126/science.aac9176
  • Primary Citation of Related Structures:  
    4JNU, 4JNV, 4JO7, 4JO9, 4JQ5, 5CWS, 5CWT, 5CWU, 5CWV, 5CWW

  • PubMed Abstract: 

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kilodalton inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin heterotrimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three-dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
sAB-158 Fab Light Chain
A, G
237Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
sAB-158 Fab Heavy Chain
B, H
266Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NSP1
C, I
208Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: NSP1CTHT_0054390
UniProt
Find proteins for G0SBQ3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SBQ3 
Go to UniProtKB:  G0SBQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SBQ3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP49
D, J
227Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: NUP49CTHT_0031980
UniProt
Find proteins for G0S4X2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S4X2 
Go to UniProtKB:  G0S4X2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S4X2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NUP57
E, K
247Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: NUP57CTHT_0010940
UniProt
Find proteins for G0S0R2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S0R2 
Go to UniProtKB:  G0S0R2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S0R2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin NIC96
F, L
74Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: NIC96CTHT_0008480
UniProt
Find proteins for G0S024 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S024 
Go to UniProtKB:  G0S024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S024
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.77 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.18α = 90
b = 162.82β = 90
c = 212.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM111461
V Foundation for Cancer ResearchUnited StatesAlbert Wyrick V Scholar Award
The Camille & Henry Dreyfus FoundationUnited StatesCamille-Dreyfus Teacher Scholar Award
Edward Mallinckrodt Jr. FoundationUnited States54th Mallinckrodt Scholar Award
Sidney Kimmel Foundation for Cancer ResearchUnited StatesKimmel Scholar Award

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Data collection
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-09-27
    Changes: Data collection
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence