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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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: 10.1038/nsmb.1931
  • Structures With Same Primary Citation

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GTP-binding nuclear protein Ran
C, F
176Homo sapiensMutation(s): 1 
Gene Names: ARA24OK/SW-cl.81RANRAN (GeneID: 5901)
Find proteins for P62826 (Homo sapiens)
Go to UniProtKB:  P62826
NIH Common Fund Data Resources
PHAROS  P62826

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Snurportin-1
B, E
361Homo sapiensMutation(s): 0 
Gene Names: PKIA (GeneID: 5569) SNUPN (GeneID: 10073)RNUT1SNUPNSPN1
Find proteins for O95149 (Homo sapiens)
Go to UniProtKB:  O95149
NIH Common Fund Data Resources
PHAROS  O95149

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exportin-1
A, D
1073Mus musculusMutation(s): 0 
Gene Names: Crm1Xpo1Xpo1 (GeneID: 103573)
Find proteins for Q6P5F9 (Mus musculus)
Go to UniProtKB:  Q6P5F9
NIH Common Fund Data Resources
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
C, F
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance