5HAX

Crystal structure of Chaetomium thermophilum Nup170 NTD-Nup53 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1126/science.aaf1015
  • Primary Citation of Related Structures:  

  • 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 under ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP170
A
742Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Gene Names: NUP170
Find proteins for G0S7B6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S7B6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nucleoporin NUP53
B
33Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Gene Names: NUP53
Find proteins for G0S156 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S156
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.230α = 90.00
b = 106.160β = 90.00
c = 120.080γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM111461
National Institutes of Health/National Institute of General Medical SciencesUnited 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 FoundationGermany--
Boehringer Ingelheim FondsGermany--
China Scholarship CouncilChina--

Revision History 

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