1M7E | pdb_00001m7e

Crystal structure of the phosphotyrosine binding domain(PTB) of mouse Disabled 2(Dab2):implications for Reeling signaling


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.273 (Depositor) 
  • R-Value Work: 
    0.244 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1M7E

This is version 1.4 of the entry. See complete history

Literature

Crystal structures of the Dab homology domains of mouse disabled 1 and 2

Yun, M.Keshvara, L.Park, C.-G.Zhang, Y.-M.Dickerson, J.B.Zheng, J.Rock, C.O.Curran, T.Park, H.-W.

(2003) J Biological Chem 278: 36572-36581

  • DOI: https://doi.org/10.1074/jbc.M304384200
  • Primary Citation Related Structures: 
    1M7E, 1OQN, 1P3R

  • PubMed Abstract: 

    Disabled (Dab) 1 and 2 are mammalian homologues of Drosophila DAB. Dab1 is a key cytoplasmic mediator in Reelin signaling that controls cell positioning in the developing central nervous system, whereas Dab2 is an adapter protein that plays a role in endocytosis. DAB family proteins possess an amino-terminal DAB homology (DH) domain that is similar to the phosphotyrosine binding/phosphotyrosine interaction (PTB/PI) domain. We have solved the structures of the DH domains of Dab2 (Dab2-DH) and Dab1 (Dab1-DH) in three different ligand forms, ligand-free Dab2-DH, the binary complex of Dab2-DH with the Asn-Pro-X-Tyr (NPXY) peptide of amyloid precursor protein (APP), and the ternary complex of Dab1-DH with the APP peptide and inositol 1,4,5-trisphosphate (Ins-1,4,5-P3, the head group of phosphatidylinositol-4,5-diphosphate (PtdIns-4,5-P2)). The similarity of these structures suggests that the rigid Dab DH domain maintains two independent pockets for binding of the APP/lipoprotein receptors and phosphoinositides. Mutagenesis confirmed the structural determinants specific for the NPXY sequence and PtdIns-4,5-P2 binding. NMR spectroscopy confirmed that the DH domain binds to Ins-1,4,5-P3 independent of the NPXY peptides. These findings suggest that simultaneous interaction of the rigid DH domain with the NPXY sequence and PtdIns-4,5-P2 plays a role in the attachment of Dab proteins to the APP/lipoprotein receptors and phosphoinositide-rich membranes.


  • Organizational Affiliation
    • Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105-2794, USA.

Macromolecule Content 

  • Total Structure Weight: 57.39 kDa 
  • Atom Count: 3,989 
  • Modeled Residue Count: 477 
  • Deposited Residue Count: 507 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Disabled homolog 2
A, B, C
160Mus musculusMutation(s): 0 
UniProt
Find proteins for P98078 (Mus musculus)
Explore P98078 
Go to UniProtKB:  P98078
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98078
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NGYENPTYK peptide
D, E, F
9N/AMutation(s): 0 
UniProt
Find proteins for P08592 (Rattus norvegicus)
Explore P08592 
Go to UniProtKB:  P08592
Entity Groups
UniProt GroupP08592
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.273 (Depositor) 
  • R-Value Work:  0.244 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.258α = 90
b = 127.258β = 90
c = 269.541γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-05
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references
  • Version 1.4: 2024-05-22
    Changes: Data collection