7TPB

p120RasGAP SH3 domain in complex with DLC1 RhoGAP domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SH3 domain regulation of RhoGAP activity: Crosstalk between p120RasGAP and DLC1 RhoGAP.

Chau, J.E.Vish, K.J.Boggon, T.J.Stiegler, A.L.

(2022) Nat Commun 13: 4788-4788

  • DOI: https://doi.org/10.1038/s41467-022-32541-4
  • Primary Citation of Related Structures:  
    7TPB

  • PubMed Abstract: 

    RhoGAP proteins are key regulators of Rho family GTPases and influence a variety of cellular processes, including cell migration, adhesion, and cytokinesis. These GTPase activating proteins (GAPs) downregulate Rho signaling by binding and enhancing the intrinsic GTPase activity of Rho proteins. Deleted in liver cancer 1 (DLC1) is a tumor suppressor and ubiquitously expressed RhoGAP protein; its activity is regulated in part by binding p120RasGAP, a GAP protein for the Ras GTPases. In this study, we report the co-crystal structure of the p120RasGAP SH3 domain bound directly to DLC1 RhoGAP, at a site partially overlapping the RhoA binding site and impinging on the catalytic arginine finger. We demonstrate biochemically that mutation of this interface relieves inhibition of RhoGAP activity by the SH3 domain. These results reveal the mechanism for inhibition of DLC1 RhoGAP activity by p120RasGAP and demonstrate the molecular basis for direct SH3 domain modulation of GAP activity.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras GTPase-activating protein 1
A, C, E, G
66Homo sapiensMutation(s): 0 
UniProt
Find proteins for B4DTL8 (Homo sapiens)
Explore B4DTL8 
Go to UniProtKB:  B4DTL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4DTL8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rho GTPase-activating protein 7
B, D, F, H
228Homo sapiensMutation(s): 0 
Gene Names: DLC1ARHGAP7KIAA1723STARD12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QB1 (Homo sapiens)
Explore Q96QB1 
Go to UniProtKB:  Q96QB1
PHAROS:  Q96QB1
GTEx:  ENSG00000164741 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QB1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.745α = 90
b = 143.745β = 90
c = 152.776γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
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 States1R01GM138411

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description