5HAX

Crystal structure of Chaetomium thermophilum Nup170 NTD-Nup53 complex

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Thermochaetoides thermophila DSM 1495
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-12-31 Released: 2016-04-20 
  • Deposition Author(s): Lin, D.H., Mobbs, G., Hoelz, A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), V Foundation for Cancer Research, Edward Mallinckrodt Jr. Foundation, Sidney Kimmel Foundation for Cancer Research, Heritage Medical Research Institute, German Research Foundation (DFG), Boehringer Ingelheim Fonds, China Scholarship Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Architecture of the symmetric core of the nuclear pore.

Lin, D.H., Stuwe, T., Schilbach, S., Rundlet, E.J., Perriches, T., Mobbs, G., Fan, Y., Thierbach, K., Huber, F.M., Collins, L.N., Davenport, A.M., Jeon, Y.E., Hoelz, A.

(2016) Science 352: aaf1015-aaf1015

  • DOI: https://doi.org/10.1126/science.aaf1015
  • Primary Citation of Related Structures:  
    5HAX, 5HAY, 5HAZ, 5HB0, 5HB1, 5HB2, 5HB3, 5HB4, 5HB5, 5HB6, 5HB7, 5HB8

  • PubMed Abstract: 

    • The nuclear pore complex (NPC) controls the transport of macromolecules between the nucleus and cytoplasm, but its molecular architecture has thus far remained poorly defined. We biochemically reconstituted NPC core protomers and elucidated the underlying protein-protein interaction network ...

    The nuclear pore complex (NPC) controls the transport of macromolecules between the nucleus and cytoplasm, but its molecular architecture has thus far remained poorly defined. We biochemically reconstituted NPC core protomers and elucidated the underlying protein-protein interaction network. Flexible linker sequences, rather than interactions between the structured core scaffold nucleoporins, mediate the assembly of the inner ring complex and its attachment to the NPC coat. X-ray crystallographic analysis of these scaffold nucleoporins revealed the molecular details of their interactions with the flexible linker sequences and enabled construction of full-length atomic structures. By docking these structures into the cryoelectron tomographic reconstruction of the intact human NPC and validating their placement with our nucleoporin interactome, we built a composite structure of the NPC symmetric core that contains ~320,000 residues and accounts for ~56 megadaltons of the NPC's structured mass. Our approach provides a paradigm for the structure determination of similarly complex macromolecular assemblies.

    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP170742Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: NUP170, CTHT_0036270
UniProt
Find proteins for G0S7B6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S7B6 
Go to UniProtKB:  G0S7B6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S7B6
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoporin NUP5333Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: NUP53, CTHT_0012410
UniProt
Find proteins for G0S156 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S156 
Go to UniProtKB:  G0S156
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S156
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.23α = 90
b = 106.16β = 90
c = 120.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM111461
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 T32 GM07616
V Foundation for Cancer ResearchUnited States--
Edward Mallinckrodt Jr. FoundationUnited States--
Sidney Kimmel Foundation for Cancer ResearchUnited States--
Heritage Medical Research InstituteUnited States--
German Research Foundation (DFG)Germany--
Boehringer Ingelheim FondsGermany--
China Scholarship CouncilChina--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-20
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2016-05-04
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence