7WFY

Crystal Structure of the VAV2 SH2 domain in complex with APP phosphorylated peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Vav2 is a novel APP-interacting protein that regulates APP protein level.

Zhang, Y.Yang, X.Liu, Y.Ge, L.Wang, J.Sun, X.Wu, B.Wang, J.

(2022) Sci Rep 12: 12752-12752

  • DOI: https://doi.org/10.1038/s41598-022-16883-z
  • Primary Citation of Related Structures:  
    7WFY

  • PubMed Abstract: 

    Amyloid precursor protein (APP) is a transmembrane protein that plays critical role in the pathogenesis of Alzheimer's disease (AD). It is also involved in many types of cancers. Increasing evidence has shown that the tyrosine phosphorylation site Y682 in the intracellular tail of APP is crucial for APP function. Here, we report that Vav2, a guanine nucleotide exchange factor (GEF) for Rho family GTPase, is a novel interaction partner of APP. We found that Vav2-SH2 domain was able to bind directly to the Y682-phosphorylated intracellular tail of APP through isothermal titration calorimetry and NMR titrating experiments. The crystal structure of Vav2-SH2 in complex with an APP-derived phosphopeptide was determined to understand the structural basis of this recognition specificity. The interaction of APP and Vav2 in a full-length manner was further confirmed in cells by GST pull-down, co-immunoprecipitation and immunofluorescence staining experiments. In addition, we found overexpression of Vav2 could inhibit APP degradation and markedly increase the protein levels of APP and its cleavage productions in 20E2 cells, and this function of Vav2 required a functional SH2 domain.


  • Organizational Affiliation

    High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide exchange factor VAV2A [auth C]117Homo sapiensMutation(s): 0 
Gene Names: VAV2
UniProt & NIH Common Fund Data Resources
Find proteins for P52735 (Homo sapiens)
Explore P52735 
Go to UniProtKB:  P52735
PHAROS:  P52735
GTEx:  ENSG00000160293 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52735
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid beta A4 protein-binding family B member 1 (protein)B [auth A]8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
GTEx:  ENSG00000142192 
Entity Groups  
UniProt GroupP05067
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
B [auth A]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.743α = 90
b = 109.589β = 90
c = 41.369γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary