6VK2

NMR solution structure of Grb2-SH2 domain at pH 7


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 66317 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The dynamics of free and phosphopeptide-bound Grb2-SH2 reveals two dynamically independent subdomains and an encounter complex with fuzzy interactions.

Sanches, K.Caruso, I.P.Almeida, F.C.L.Melo, F.A.

(2020) Sci Rep 10: 13040-13040

  • DOI: https://doi.org/10.1038/s41598-020-70034-w
  • Primary Citation of Related Structures:  
    6VK2

  • PubMed Abstract: 

    The growth factor receptor-bound protein 2 (Grb2) is a key factor in the regulation of cell survival, proliferation, differentiation, and metabolism. In its structure, the central Src homology 2 (SH2) domain is flanked by two Src homology 3 (SH3). SH2 is the most important domain in the recognition of phosphotyrosines. Here, we present the first dynamical characterization of Grb2-SH2 domain in the free state and in the presence of phosphopeptide EpYINSQV at multiple timescales, which revealed valuable information to the understanding of phophotyrosine sensing mechanism. Grb2-SH2 presented two dynamically independent subdomains, subdomain I involved in pY recognition and subdomain II is the pY + 2 specificity pocket. Under semi-saturated concentrations of pY-pep we observed fuzzy interactions, which led to chemical exchange observed by NMR. This information was used to describe the encounter complex. The association with pY-pep is dynamic, involving fuzzy interactions and multiple conformations of pY-pep with negative and hydrophobic residues, creating an electrostatic-potential that drives the binding of pY-pep. The recognition face is wider than the binding site, with many residues beyond the central SH2 binding site participating in the association complex, which contribute to explain previously reported capability of Grb2 to recognize remote pY.


  • Organizational Affiliation

    National Center for Structural Biology and Bioimaging (CENABIO)/National Center for Nuclear Magnetic Resonance (CNRMN), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Growth factor receptor-bound protein 296Homo sapiensMutation(s): 0 
Gene Names: GRB2ASH
UniProt & NIH Common Fund Data Resources
Find proteins for P62993 (Homo sapiens)
Explore P62993 
Go to UniProtKB:  P62993
GTEx:  ENSG00000177885 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62993
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 66317 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/17630-0
Sao Paulo Research Foundation (FAPESP)Brazil2017/20642-8
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil442951/2014-0
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil309564/2017-4

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-08-19
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Database references, Other