9BZ4 | pdb_00009bz4

Crystal structure of the C2 and GAP domains of human p120RasGAP

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2024-05-24 Released: 2025-01-22 
  • Deposition Author(s): Paul, M.E., Boggon, T.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.284 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Models: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The C2 domain augments Ras GTPase-activating protein catalytic activity.

Paul, M.E.Chen, D.Vish, K.J.Lartey, N.L.Hughes, E.Freeman, Z.T.Saunders, T.L.Stiegler, A.L.King, P.D.Boggon, T.J.

(2025) Proc Natl Acad Sci U S A 122: e2418433122-e2418433122

  • DOI: https://doi.org/10.1073/pnas.2418433122
  • Primary Citation of Related Structures:  
    9BZ4

  • PubMed Abstract: 

    Regulation of Ras GTPases by GTPase-activating proteins (GAPs) is essential for their normal signaling. Nine of the ten GAPs for Ras contain a C2 domain immediately proximal to their canonical GAP domain, and in RasGAP (p120GAP, p120RasGAP; RASA1 ) mutation of this domain is associated with vascular malformations in humans. Here, we show that the C2 domain of RasGAP is required for full catalytic activity toward Ras. Analyses of the RasGAP C2-GAP crystal structure, AlphaFold models, and sequence conservation reveal direct C2 domain interaction with the Ras allosteric lobe. This is achieved by an evolutionarily conserved surface centered around RasGAP residue R707, point mutation of which impairs the catalytic advantage conferred by the C2 domain in vitro. In mice, R707C mutation phenocopies the vascular and signaling defects resulting from constitutive disruption of the RASA1 gene. In SynGAP, mutation of the equivalent conserved C2 domain surface impairs catalytic activity. Our results indicate that the C2 domain is required to achieve full catalytic activity of GAPs for Ras.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras GTPase-activating protein 1
A, B, C, D
468Homo sapiensMutation(s): 0 
Gene Names: RASA1GAPRASA
UniProt & NIH Common Fund Data Resources
Find proteins for P20936 (Homo sapiens)
Explore P20936 
Go to UniProtKB:  P20936
PHAROS:  P20936
GTEx:  ENSG00000145715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20936
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.284 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.894α = 95.81
b = 94.036β = 111.1
c = 96.713γ = 108.51
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM138411
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States1R01NS117609
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM102262
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesT32GM007324

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references