2QNA | pdb_00002qna

Crystal structure of human Importin-beta (127-876) in complex with the IBB-domain of Snurportin1 (1-65)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 
    0.282 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2QNA

This is version 1.3 of the entry. See complete history

Literature

Structural basis for RanGTP independent entry of spliceosomal U snRNPs into the nucleus.

Wohlwend, D.Strasser, A.Dickmanns, A.Ficner, R.

(2007) J Mol Biology 374: 1129-1138

  • DOI: https://doi.org/10.1016/j.jmb.2007.09.065
  • Primary Citation Related Structures: 
    2QNA

  • PubMed Abstract: 

    The nuclear import of assembled spliceosomal subunits, the uridine-rich small nuclear ribonucleoprotein particles (U snRNPs), is mediated by a nuclear import receptor adaptor couple of importin beta (Imp beta) and snurportin1 (SPN1). In contrast to any other characterized active nuclear import, the Imp beta/SPN1/U snRNP complex does not require RanGTP for the terminal release from the nuclear basket of the nuclear pore complex (NPC). The crystal structure of Imp beta (127-876) in complex with the Imp beta-binding (IBB) domain of SPN1 (1-65) at 2.8-A resolution reveals that Imp beta adopts an open conformation, which is unique for a functional Imp beta/cargo complex, and rather surprisingly, it resembles the conformation of the Imp beta/RanGTP complex. As binding of RanGTP to Imp beta usually triggers the release of import complexes from the NPC, we propose that by already mimicking a conformation similar to Imp beta/RanGTP the independent dissociation of Imp beta/SPN1 from the nuclear basket is energetically aided.


  • Organizational Affiliation
    • Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik and GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 92.44 kDa 
  • Atom Count: 6,090 
  • Modeled Residue Count: 774 
  • Deposited Residue Count: 828 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit beta-1762Homo 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-166Homo sapiensMutation(s): 0 
Gene Names: SNUPNRNUT1SPN1
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: 2.84 Å
  • R-Value Free:  0.282 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.22α = 90
b = 79.07β = 90
c = 208.46γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Advisory, Data collection, Database references, Derived calculations