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: 10.1126/science.aac9176
  • Primary Citation of Related Structures:  
    4JNU, 4JNV, 4JO7, 4JO9, 4JQ5, 5CWT, 5CWS, 5CWV, 5CWU, 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 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. hoelz@caltech.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
sAB-158 Fab Light ChainA, G237Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
sAB-158 Fab Heavy ChainB, H266Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NSP1C, I208Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: NSP1CTHT_0054390
UniProt
Find proteins for G0SBQ3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0SBQ3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP49D, J227Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: NUP49CTHT_0031980
UniProt
Find proteins for G0S4X2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0S4X2
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP57E, K247Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: NUP57CTHT_0010940
UniProt
Find proteins for G0S0R2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0S0R2
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NIC96F, L74Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 0 
Gene Names: NIC96CTHT_0008480
UniProt
Find proteins for G0S024 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Go to UniProtKB:  G0S024
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OS
Query on OS

Download Ideal Coordinates CCD File 
M [auth C], N [auth I]OSMIUM ION
Os
XQBKHDFIPARBOX-UHFFFAOYSA-N
 Ligand Interaction
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

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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 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