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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
sAB-158 Fab Light Chain
A, G
237N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
sAB-158 Fab Heavy Chain
B, H
266N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NSP1
C, I
208Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Gene Names: NSP1
Find proteins for G0SBQ3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SBQ3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP49
D, J
227Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Gene Names: NUP49
Find proteins for G0S4X2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S4X2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP57
E, K
247Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Gene Names: NUP57
Find proteins for G0S0R2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S0R2
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NIC96
F, L
74Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Gene Names: NIC96
Find proteins for G0S024 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S024
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OS
Query on OS
Download SDF File 
Download CCD File 
C, 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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 123.180α = 90.00
b = 162.820β = 90.00
c = 212.870γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited 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 

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