3EA5

Kap95p Binding Induces the Switch Loops of RanGDP to adopt the GTP-bound Conformation: Implications for Nuclear Import Complex Assembly Dynamics


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Kap95p binding induces the switch loops of RanGDP to adopt the GTP-bound conformation: implications for nuclear import complex assembly dynamics.

Forwood, J.K.Lonhienne, T.G.Marfori, M.Robin, G.Meng, W.Guncar, G.Liu, S.M.Stewart, M.Carroll, B.J.Kobe, B.

(2008) J Mol Biol 383: 772-782

  • DOI: https://doi.org/10.1016/j.jmb.2008.07.090
  • Primary Citation of Related Structures:  
    3EA5

  • PubMed Abstract: 

    The asymmetric distribution of the nucleotide-bound state of Ran across the nuclear envelope is crucial for determining the directionality of nuclear transport. In the nucleus, Ran is primarily in the guanosine 5'-triphosphate (GTP)-bound state, whereas in the cytoplasm, Ran is primarily guanosine 5'-diphosphate (GDP)-bound. Conformational changes within the Ran switch I and switch II loops are thought to modulate its affinity for importin-beta. Here, we show that RanGDP and importin-beta form a stable complex with a micromolar dissociation constant. This complex can be dissociated by importin-beta binding partners such as importin-alpha. Surprisingly, the crystal structure of the Kap95p-RanGDP complex shows that Kap95p induces the switch I and II regions of RanGDP to adopt a conformation that resembles that of the GTP-bound form. The structure of the complex provides insights into the structural basis for the gradation of affinities regulating nuclear protein transport.


  • Organizational Affiliation

    School of Biomedical Sciences, Charles Sturt University, Wagga Wagga 2650, Australia. jforwood@csu.edu.au


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran
A, C
216Homo sapiensMutation(s): 1 
Gene Names: RANARA24
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
GTEx:  ENSG00000132341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62826
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Importin subunit beta-1
B, D
861Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: KAP95
UniProt
Find proteins for Q06142 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06142 
Go to UniProtKB:  Q06142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06142
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.85α = 90
b = 127.81β = 90
c = 171.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-02-21
    Changes: Data collection