3BRW

Structure of the Rap-RapGAP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Rap-RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues

Scrima, A.Thomas, C.Deaconescu, D.Wittinghofer, A.

(2008) EMBO J 27: 1145-1153

  • DOI: https://doi.org/10.1038/emboj.2008.30
  • Primary Citation of Related Structures:  
    3BRW

  • PubMed Abstract: 

    The GTP-binding protein Rap1 regulates integrin-mediated and other cell adhesion processes. Unlike most other Ras-related proteins, it contains a threonine in switch II instead of a glutamine (Gln61 in Ras), a residue crucial for the GTPase reaction of most G proteins. Furthermore, unlike most other GTPase-activating proteins (GAPs) for small G proteins, which supply a catalytically important Arg-finger, no arginine residue of RapGAP makes a significant contribution to the GTPase reaction of Rap1. For a detailed understanding of the reaction mechanism, we have solved the structure of Rap1 in complex with Rap1GAP. It shows that the Thr61 of Rap is away from the active site and that an invariant asparagine of RapGAPs, the Asn-thumb, takes over the role of the cis-glutamine of Ras, Rho or Ran. The structure and biochemical data allow to further explain the mechanism and to define the important role of a conserved tyrosine. The structure and biochemical data furthermore show that the RapGAP homologous region of the tumour suppressor Tuberin is sufficient for catalysis on Rheb.


  • Organizational Affiliation

    Department of Structural Biology, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rap1 GTPase-activating protein 1
A, B, C
341Homo sapiensMutation(s): 1 
Gene Names: RAP1GAP
UniProt & NIH Common Fund Data Resources
Find proteins for P47736 (Homo sapiens)
Explore P47736 
Go to UniProtKB:  P47736
GTEx:  ENSG00000076864 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47736
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rap-1b167Homo sapiensMutation(s): 0 
Gene Names: RAP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P61224 (Homo sapiens)
Explore P61224 
Go to UniProtKB:  P61224
GTEx:  ENSG00000127314 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61224
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.723α = 90
b = 209.723β = 90
c = 108.217γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description