1K5D

Crystal structure of Ran-GPPNHP-RanBP1-RanGAP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

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This is version 1.3 of the entry. See complete history


Literature

RanGAP mediates GTP hydrolysis without an arginine finger.

Seewald, M.J.Korner, C.Wittinghofer, A.Vetter, I.R.

(2002) Nature 415: 662-666

  • DOI: https://doi.org/10.1038/415662a
  • Primary Citation of Related Structures:  
    1K5D, 1K5G

  • PubMed Abstract: 

    GTPase-activating proteins (GAPs) increase the rate of GTP hydrolysis on guanine nucleotide-binding proteins by many orders of magnitude. Studies with Ras and Rho have elucidated the mechanism of GAP action by showing that their catalytic machinery is both stabilized by GAP binding and complemented by the insertion of a so-called 'arginine finger' into the phosphate-binding pocket. This has been proposed as a universal mechanism for GAP-mediated GTP hydrolysis. Ran is a nuclear Ras-related protein that regulates both transport between the nucleus and cytoplasm during interphase, and formation of the mitotic spindle and/or nuclear envelope in dividing cells. Ran-GTP is hydrolysed by the combined action of Ran-binding proteins (RanBPs) and RanGAP. Here we present the three-dimensional structure of a Ran-RanBP1-RanGAP ternary complex in the ground state and in a transition-state mimic. The structure and biochemical experiments show that RanGAP does not act through an arginine finger, that the basic machinery for fast GTP hydrolysis is provided exclusively by Ran and that correct positioning of the catalytic glutamine is essential for catalysis.


  • Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abteilung Strukturelle Biologie, Dortmund, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein RAN
A, D, G, J
216Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
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Go to UniProtKB:  P62826
GTEx:  ENSG00000132341 
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UniProt GroupP62826
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein
B, E, H, K
201Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P43487 (Homo sapiens)
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Go to UniProtKB:  P43487
GTEx:  ENSG00000099901 
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UniProt GroupP43487
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ran GTPase activating protein 1
C, F, I, L
386Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P41391 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P41391 
Go to UniProtKB:  P41391
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UniProt GroupP41391
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.551α = 71.59
b = 103.109β = 80.55
c = 120.177γ = 67.78
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
ProDCdata collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description