3NBY

Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 

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Literature

NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.

Guttler, T.Madl, T.Neumann, P.Deichsel, D.Corsini, L.Monecke, T.Ficner, R.Sattler, M.Gorlich, D.

(2010) Nat Struct Mol Biol 17: 1367-1376

  • DOI: https://doi.org/10.1038/nsmb.1931
  • Primary Citation of Related Structures:  
    2L1L, 3NBY, 3NBZ, 3NC0, 3NC1

  • PubMed Abstract: 

    Classic nuclear export signals (NESs) confer CRM1-dependent nuclear export. Here we present crystal structures of the RanGTP-CRM1 complex alone and bound to the prototypic PKI or HIV-1 Rev NESs. These NESs differ markedly in the spacing of their key hydrophobic (Φ) residues, yet CRM1 recognizes them with the same rigid set of five Φ pockets. The different Φ spacings are compensated for by different conformations of the bound NESs: in the case of PKI, an α-helical conformation, and in the case of Rev, an extended conformation with a critical proline docking into a Φ pocket. NMR analyses of CRM1-bound and CRM1-free PKI NES suggest that CRM1 selects NES conformers that pre-exist in solution. Our data lead to a new structure-based NES consensus, and explain why NESs differ in their affinities for CRM1 and why supraphysiological NESs bind the exportin so tightly.


  • Organizational Affiliation

    Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Snurportin-1A [auth B],
D [auth E]
361Homo sapiensMutation(s): 0 
Gene Names: PKIA (GeneID: 5569) SNUPN (GeneID: 10073)RNUT1SNUPNSPN1
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Find proteins for O95149 (Homo sapiens)
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Go to UniProtKB:  O95149
GTEx:  ENSG00000169371 
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UniProt GroupO95149
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanB [auth C],
E [auth F]
176Homo sapiensMutation(s): 1 
Gene Names: ARA24OK/SW-cl.81RANRAN (GeneID: 5901)
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Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
GTEx:  ENSG00000132341 
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UniProt GroupP62826
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-1C [auth A],
F [auth D]
1,073Mus musculusMutation(s): 0 
Gene Names: Crm1Xpo1Xpo1 (GeneID: 103573)
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Find proteins for Q6P5F9 (Mus musculus)
Explore Q6P5F9 
Go to UniProtKB:  Q6P5F9
IMPC:  MGI:2144013
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UniProt GroupQ6P5F9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.261 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.09α = 90
b = 223.726β = 100.63
c = 163.064γ = 90
Software Package:
Software NamePurpose
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-06
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description