6Q84

Crystal structure of RanGTP-Pdr6-eIF5A export complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.227 

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Literature

Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122.

Aksu, M.Trakhanov, S.Vera Rodriguez, A.Gorlich, D.

(2019) J Cell Biol 218: 1839-1852

  • DOI: https://doi.org/10.1083/jcb.201812093
  • Primary Citation of Related Structures:  
    6Q82, 6Q83, 6Q84

  • PubMed Abstract: 

    Importins ferry proteins into nuclei while exportins carry cargoes to the cytoplasm. In the accompanying paper in this issue (Vera Rodriguez et al. 2019. J. Cell Biol. https://doi.org/10.1083/jcb.201812091), we discovered that Pdr6 is a biportin that imports, e.g., the SUMO E2 ligase Ubc9 while depleting the translation factor eIF5A from the nuclear compartment. In this paper, we report the structures of key transport intermediates, namely, of the Ubc9•Pdr6 import complex, of the RanGTP•Pdr6 heterodimer, and of the trimeric RanGTP•Pdr6•eIF5A export complex. These revealed nonlinear transport signals, chaperone-like interactions, and how the RanGTPase system drives Pdr6 to transport Ubc9 and eIF5A in opposite directions. The structures also provide unexpected insights into the evolution of transport selectivity. Specifically, they show that recognition of Ubc9 by Pdr6 differs fundamentally from that of the human Ubc9-importer Importin 13. Likewise, Pdr6 recognizes eIF5A in a nonhomologous manner compared with the mammalian eIF5A-exporter Exportin 4. This suggests that the import of Ubc9 and active nuclear exclusion of eIF5A evolved in different eukaryotic lineages more than once and independently from each other.


  • Organizational Affiliation

    Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Importin beta-like protein KAP122
A, D
1,080Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: KAP122PDR6YGL016W
UniProt
Find proteins for P32767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32767 
Go to UniProtKB:  P32767
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32767
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran
B, E
176Homo sapiensMutation(s): 1 
Gene Names: RANARA24OK/SW-cl.81
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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A-1
C, F
142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HYP2TIF51AYEL034WSYGP-ORF21
UniProt
Find proteins for P23301 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P23301 
Go to UniProtKB:  P23301
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23301
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.227 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.54α = 90
b = 139.54β = 90
c = 346.57γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
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: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-12
    Changes: Data collection, Database references