3ZJY

Crystal Structure of Importin 13 - RanGTP - eIF1A complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Nuclear Export Activity of Importin13.

Grunwald, M.Lazzaretti, D.Bono, F.

(2013) EMBO J 32: 899

  • DOI: https://doi.org/10.1038/emboj.2013.29
  • Primary Citation of Related Structures:  
    3ZJY, 3ZKV

  • PubMed Abstract: 

    Importin13 (Imp13) is a bidirectional karyopherin that can mediate both import and export of cargoes. Imp13 recognizes several import cargoes, which include the exon junction complex components Mago-Y14 and the E2 SUMO-conjugating enzyme Ubc9, and one known export cargo, the translation initiation factor 1A (eIF1A). To understand how Imp13 can perform double duty, we determined the 3.6-Å crystal structure of Imp13 in complex with RanGTP and with eIF1A. eIF1A binds at the inner surface of the Imp13 C-terminal arch adjacent and concomitantly to RanGTP illustrating how eIF1A can be exported by Imp13. Moreover, the 3.0-Å structure of Imp13 in its unbound state reveals the existence of an open conformation in the cytoplasm that explains export cargo release and completes the export branch of the Imp13 pathway. Finally, we demonstrate that Imp13 is able to bind and export eIF1A in vivo and that its function is essential.


  • Organizational Affiliation

    Max Planck Institute for Developmental Biology, Tübingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-BINDING NUCLEAR PROTEIN RAN
A, D, F
180Homo sapiensMutation(s): 1 
EC: 3.6.5
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IMPORTIN-13
B, E, G
963Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O94829 (Homo sapiens)
Explore O94829 
Go to UniProtKB:  O94829
PHAROS:  O94829
GTEx:  ENSG00000117408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94829
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 1A, X-CHROMOSOMAL112Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P47813 (Homo sapiens)
Explore P47813 
Go to UniProtKB:  P47813
PHAROS:  P47813
GTEx:  ENSG00000173674 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47813
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.5α = 90
b = 100.4β = 90.91
c = 274.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description