8DGQ

Crystal structure of p120RasGAP SH2-SH3-SH2 in complex with p190RhoGAP doubly phosphorylated peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Tandem engagement of phosphotyrosines by the dual SH2 domains of p120RasGAP.

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

(2022) Structure 30: 1603-1614.e5

  • DOI: https://doi.org/10.1016/j.str.2022.10.009
  • Primary Citation of Related Structures:  
    8DGQ

  • PubMed Abstract: 

    p120RasGAP is a multidomain GTPase-activating protein for Ras. The presence of two Src homology 2 domains in an SH2-SH3-SH2 module raises the possibility that p120RasGAP simultaneously binds dual phosphotyrosine residues in target proteins. One known binding partner with two proximal phosphotyrosines is p190RhoGAP, a GTPase-activating protein for Rho GTPases. Here, we present the crystal structure of the p120RasGAP SH2-SH3-SH2 module bound to a doubly tyrosine-phosphorylated p190RhoGAP peptide, revealing simultaneous phosphotyrosine recognition by the SH2 domains. The compact arrangement places the SH2 domains in close proximity resembling an SH2 domain tandem and exposed SH3 domain. Affinity measurements support synergistic binding, while solution scattering reveals that dual phosphotyrosine binding induces compaction of this region. Our studies reflect a binding mode that limits conformational flexibility within the SH2-SH3-SH2 cassette and relies on the spacing and sequence surrounding the two phosphotyrosines, potentially representing a selectivity mechanism for downstream signaling events.


  • Organizational Affiliation

    Department of Pharmacology, 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, B
273Homo 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rho GTPase-activating protein 35C [auth U],
D [auth V]
29Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRY4 (Homo sapiens)
Explore Q9NRY4 
Go to UniProtKB:  Q9NRY4
PHAROS:  Q9NRY4
GTEx:  ENSG00000160007 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRY4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
C [auth U],
D [auth V]
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.21α = 90
b = 113.5β = 90
c = 119.07γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
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 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: 2022-11-02
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection