1K5G

Crystal structure of Ran-GDP-AlFx-RanBP1-RanGAP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1038/415662a
  • Primary Citation of Related Structures:  
    1K5G, 1K5D

  • 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 ...

    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.


    Related Citations: 
    • THE RAS-RASGAP COMPLEX: STRUCTURAL BASIS FOR GTPASE ACTIVATION AND ITS LOSS IN ONCOGENIC RAS MUTANTS
      Scheffzek, K., Ahmadian, M.R., Kabsch, W., Wiesmueller, L., Lautwein, A., Schmitz, F., Wittinghofer, A.
      (1997) Science 277: 333
    • STRUCTURE OF A RAN-BINDING DOMAIN COMPLEXED WITH RAN BOUND TO A GTP ANALOGUE: IMPLICATIONS FOR NUCLEAR TRANSPORT
      Vetter, I.R., Nowak, C., Nishimoto, T., Kuhlmann, J., Wittinghofer, A.
      (1999) Nature 398: 39
    • THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN
      Hillig, R.C., Renault, L., Vetter, I.R., Drell, T., Wittinghofer, A., Becker, J.
      (1999) Mol Cell 3: 781
    • RNA1 ENCODES A GTPASE-ACTIVATING PROTEIN SPECIFIC FOR GSP1P, THE RAN/TC4 HOMOLOGUE OF SACCHAROMYCES CEREVISIAE
      Becker, J., Melchior, F., Gerke, V., Bischoff, F.R., Ponstingl, H., Wittinghofer, A.
      (1995) J Biol Chem 270: 11860
    • THE ACIDIC C-TERMINAL DOMAIN OF RNA1P IS REQUIRED FOR THE BINDING OF RAN.GTP AND FOR RANGAP ACTIVITY
      Haberland, J., Becker, J., Gerke, V.
      (1997) J Biol Chem 272: 24717

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein RANADGJ216Homo sapiensMutation(s): 0 
Gene Names: RANARA24OK/SW-cl.81
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
NIH Common Fund Data Resources
PHAROS  P62826
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ran-specific GTPase-activating proteinBEHK201Homo sapiensMutation(s): 0 
Gene Names: RANBP1
Find proteins for P43487 (Homo sapiens)
Explore P43487 
Go to UniProtKB:  P43487
NIH Common Fund Data Resources
PHAROS  P43487
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ran GTPase activating protein 1CFIL386Schizosaccharomyces pombeMutation(s): 0 
Find proteins for P41391 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P41391 
Go to UniProtKB:  P41391
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download CCD File 
A, D, G, J
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
AF3
Query on AF3

Download CCD File 
A, D, G, J
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, D, G, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.93α = 71.67
b = 102.568β = 79.09
c = 118.85γ = 67.81
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
PRODCdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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