6XA6

Crystal Structure of Human Scribble PDZ3:Vangl2 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of the human Scribble-Vangl2 association in health and disease.

How, J.Y.Stephens, R.K.Lim, K.Y.B.Humbert, P.O.Kvansakul, M.

(2021) Biochem J 478: 1321-1332

  • DOI: https://doi.org/10.1042/BCJ20200816
  • Primary Citation of Related Structures:  
    6XA6, 6XA7, 6XA8, 7JO7

  • PubMed Abstract: 

    Scribble is a critical cell polarity regulator that has been shown to work as either an oncogene or tumor suppressor in a context dependent manner, and also impacts cell migration, tissue architecture and immunity. Mutations in Scribble lead to neural tube defects in mice and humans, which has been attributed to a loss of interaction with the planar cell polarity regulator Vangl2. We show that the Scribble PDZ domains 1, 2 and 3 are able to interact with the C-terminal PDZ binding motif of Vangl2 and have now determined crystal structures of these Scribble PDZ domains bound to the Vangl2 peptide. Mapping of mammalian neural tube defect mutations reveal that mutations located distal to the canonical PDZ domain ligand binding groove can not only ablate binding to Vangl2 but also disrupt binding to multiple other signaling regulators. Our findings suggest that PDZ-associated neural tube defect mutations in Scribble may not simply act in a Vangl2 dependent manner but as broad-spectrum loss of function mutants by disrupting the global Scribble-mediated interaction network.


  • Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein scribble homologA [auth B],
C [auth A]
96Homo sapiensMutation(s): 0 
Gene Names: SCRIBCRIB1KIAA0147LAP4SCRB1VARTUL
UniProt & NIH Common Fund Data Resources
Find proteins for Q14160 (Homo sapiens)
Explore Q14160 
Go to UniProtKB:  Q14160
PHAROS:  Q14160
GTEx:  ENSG00000180900 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14160
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vang-like protein 2B [auth C],
D
8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULK5 (Homo sapiens)
Explore Q9ULK5 
Go to UniProtKB:  Q9ULK5
PHAROS:  Q9ULK5
GTEx:  ENSG00000162738 
Entity Groups  
UniProt GroupQ9ULK5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.706α = 90
b = 54.706β = 90
c = 129.979γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1103871
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1079133
Australian Research Council (ARC)AustraliaFT130101349

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description