3IBV | pdb_00003ibv

Karyopherin cytosolic state

• PDB DOI: https://doi.org/10.2210/pdb3IBV/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-17 Released: 2009-08-25 
• Deposition Author(s): Cook, A.G., Fukuhara, N., Jinek, M., Conti, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.313 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.275 (Depositor), 0.278 (DCC) 

Literature

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

• PubMed: 19680239 
• DOI: https://doi.org/10.1038/nature08394
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Cell Biology, MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 220.87 kDa 
• Atom Count: 12,876 
• Modeled Residue Count: 1,819 
• Deposited Residue Count: 1,960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exportin-T	A, B	980	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: los1, SPBP8B7.09c
UniProt
Find proteins for O94258 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O94258  Go to UniProtKB:  O94258

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.313 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.275 (Depositor), 0.278 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.9	α = 90
b = 130.1	β = 90
c = 173.9	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Cook, A.G., Fukuhara, N., Jinek, M., Conti, E.

Revision History  

• 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