Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural Basis for Selective Binding of Export Cargoes by Exportin-5

Yamazawa, R.Jiko, C.Choi, S.Park, I.Y.Nakagawa, A.Yamashita, E.Lee, S.J.

(2018) Structure 26: 1393-1398.e2

  • DOI: https://doi.org/10.1016/j.str.2018.06.014
  • Primary Citation of Related Structures:  
    5YU6, 5YU7

  • PubMed Abstract: 

    In the nucleus, RanGTP binding to importin dissociates the cargo. On the other hand, RanGTP enables exportin to bind export cargo and form the export complex by each exportin's own cargo selection mechanism. Here, we present two X-ray structures for Exportin-5 (Exp-5) alone and Exp-5:RanGTP intermediate complex. The structure of Exp-5 adopts a ring-shaped closed conformation by C-terminal anchor residues 1,167-1,179, interacting with N-terminal heat repeats 4-9. The closed form of Exp-5 is important for the stability of the cargo-free state. Interaction between Exp-5 and RanGTP induces elimination of intramolecular contacts of the C-terminal anchor. A large movement of N-terminal 1-9th heat repeats and C-terminal 19-20th heat repeats creates an open space for RanGTP accommodation. Exp-5 in Exp-5:RanGTP and Exp-5:RanGTP:pre-miRNA adopts the same conformation. RanGTP binding to Exp-5 creates a selective molecular cage area for accepting its cargoes, such as small double-stranded RNAs, without conformational change in Exp-5:RanGTP.

  • Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-51,204Homo sapiensMutation(s): 0 
Gene Names: XPO5KIAA1291RANBP21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAV4 (Homo sapiens)
Explore Q9HAV4 
Go to UniProtKB:  Q9HAV4
GTEx:  ENSG00000124571 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HAV4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 286.163α = 90
b = 286.163β = 90
c = 59.349γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
NRFKorea, Republic OfMEST 2011-0017405

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2021-07-07
    Changes: Database references, Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description