2Q5D | pdb_00002q5d

Crystal Structure of Human Importin Beta bound to the Snurportin1 IBB-domain second crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.328 (Depositor), 0.307 (DCC) 
  • R-Value Work: 
    0.303 (Depositor), 0.296 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Molecular Basis for the Recognition of Snurportin 1 by Importin {beta}.

Mitrousis, G.Olia, A.S.Walker-Kopp, N.Cingolani, G.

(2008) J Biological Chem 283: 7877-7884

  • DOI: https://doi.org/10.1074/jbc.M709093200
  • Primary Citation Related Structures: 
    2P8Q, 2Q5D

  • PubMed Abstract: 

    The nuclear import of uridine-rich ribonucleoproteins is mediated by the transport adaptor snurportin 1 (SNP1). Similar to importin alpha, SNP1 uses an N-terminal importin beta binding (sIBB) domain to recruit the receptor importin beta and gain access to the nucleus. In this study, we demonstrate that the sIBB domain has a bipartite nature, which contains two distinct binding determinants for importin beta. The first determinant spans residues 25-65 and includes the previously identified importin alpha IBB (alphaIBB) region of homology. The second binding determinant encompasses residues 1-24 and resembles region 1011-1035 of the nucleoporin 153 (Nup153). The two binding determinants synergize within the sIBB domain to confer a low nanomolar binding affinity for importin beta (K(d) approximately 2 nm) in an interaction that, in vitro, is displaced by RanGTP. We propose that in vivo the synergy of Nup153 and nuclear RanGTP promotes translocation of uridine-rich ribonucleoproteins into the nucleus.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210, USA.

Macromolecule Content 

  • Total Structure Weight: 204.57 kDa 
  • Atom Count: 13,750 
  • Modeled Residue Count: 1,775 
  • Deposited Residue Count: 1,832 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin beta-1 subunitA,
C [auth B]
876Homo sapiensMutation(s): 0 
Gene Names: KPNB1NTF97
UniProt & NIH Common Fund Data Resources
Find proteins for Q14974 (Homo sapiens)
Explore Q14974 
Go to UniProtKB:  Q14974
PHAROS:  Q14974
GTEx:  ENSG00000108424 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14974
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Snurportin-1B [auth C],
D
40Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O95149 (Homo sapiens)
Explore O95149 
Go to UniProtKB:  O95149
GTEx:  ENSG00000169371 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95149
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.328 (Depositor), 0.307 (DCC) 
  • R-Value Work:  0.303 (Depositor), 0.296 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.985α = 90
b = 100.696β = 109.23
c = 108.68γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-04-02
    Changes: Source and taxonomy
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description