Karyopherin cytosolic state

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.275 

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Structures of the tRNA export factor in the nuclear and cytosolic states

Cook, A.G.Fukuhara, N.Jinek, M.Conti, E.

(2009) Nature 461: 60-65

  • DOI: https://doi.org/10.1038/nature08394
  • Primary Citation of Related Structures:  
    3IBV, 3ICQ

  • PubMed Abstract: 

    Transfer RNAs are among the most ubiquitous molecules in cells, central to decoding information from messenger RNAs on translating ribosomes. In eukaryotic cells, tRNAs are actively transported from their site of synthesis in the nucleus to their site of function in the cytosol. This is mediated by a dedicated nucleo-cytoplasmic transport factor of the karyopherin-beta family (Xpot, also known as Los1 in Saccharomyces cerevisiae). Here we report the 3.2 A resolution structure of Schizosaccharomyces pombe Xpot in complex with tRNA and RanGTP, and the 3.1 A structure of unbound Xpot, revealing both nuclear and cytosolic snapshots of this transport factor. Xpot undergoes a large conformational change on binding cargo, wrapping around the tRNA and, in particular, binding to the tRNA 5' and 3' ends. The binding mode explains how Xpot can recognize all mature tRNAs in the cell and yet distinguish them from those that have not been properly processed, thus coupling tRNA export to quality control.

  • Organizational Affiliation

    Structural Cell Biology, MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
980Schizosaccharomyces pombeMutation(s): 0 
Gene Names: los1SPBP8B7.09c
Find proteins for O94258 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94258 
Go to UniProtKB:  O94258
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94258
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.275 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.9α = 90
b = 130.1β = 90
c = 173.9γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations