4JQ5 | pdb_00004jq5

Crystal structure of the human Nup49CCS2+3* coiled-coil segment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 
    0.293 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.285 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 
    0.285 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4JQ5

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: https://doi.org/10.1126/science.aac9176
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 121.66 kDa 
  • Atom Count: 8,526 
  • Modeled Residue Count: 1,027 
  • Deposited Residue Count: 1,032 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoporin p58/p45
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
86Homo sapiensMutation(s): 0 
Gene Names: NUPL1KIAA0410
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVL2 (Homo sapiens)
Explore Q9BVL2 
Go to UniProtKB:  Q9BVL2
PHAROS:  Q9BVL2
GTEx:  ENSG00000139496 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVL2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free:  0.293 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.285 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 0.285 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.82α = 120.04
b = 77.097β = 90.12
c = 77.197γ = 89.96
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Structure summary
  • Version 1.2: 2016-02-03
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references