3L6X | pdb_00003l6x

Crystal structure of p120 catenin in complex with E-cadherin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.234 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.201 (Depositor) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3L6X

This is version 1.3 of the entry. See complete history

Literature

Dynamic and static interactions between p120 catenin and E-cadherin regulate the stability of cell-cell adhesion.

Ishiyama, N.Lee, S.H.Liu, S.Li, G.Y.Smith, M.J.Reichardt, L.F.Ikura, M.

(2010) Cell 141: 117-128

  • DOI: https://doi.org/10.1016/j.cell.2010.01.017
  • Primary Citation Related Structures: 
    3L6X, 3L6Y

  • PubMed Abstract: 

    The association of p120 catenin (p120) with the juxtamembrane domain (JMD) of the cadherin cytoplasmic tail is critical for the surface stability of cadherin-catenin cell-cell adhesion complexes. Here, we present the crystal structure of p120 isoform 4A in complex with the JMD core region (JMD(core)) of E-cadherin. The p120 armadillo repeat domain contains modular binding pockets that are complementary to electrostatic and hydrophobic properties of the JMD(core). Single-residue mutations within the JMD(core)-binding site of p120 abolished its interaction with E- and N-cadherins in vitro and in cultured cells. These mutations of p120 enabled us to clearly differentiate between N-cadherin-dependent and -independent steps of neuronal dendritic spine morphogenesis crucial for synapse development. NMR studies revealed that p120 regulates the stability of cadherin-mediated cell-cell adhesion by associating with the majority of the JMD, including residues implicated in clathrin-mediated endocytosis and Hakai-dependent ubiquitination of E-cadherin, through its discrete "dynamic" and "static" binding sites.


  • Organizational Affiliation
    • Division of Signaling Biology, Ontario Cancer Institute, ON, Canada.

Macromolecule Content 

  • Total Structure Weight: 67.75 kDa 
  • Atom Count: 3,664 
  • Modeled Residue Count: 452 
  • Deposited Residue Count: 602 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Catenin delta-1584Homo sapiensMutation(s): 0 
Gene Names: CTNND1KIAA0384
UniProt & NIH Common Fund Data Resources
Find proteins for O60716 (Homo sapiens)
Explore O60716 
Go to UniProtKB:  O60716
PHAROS:  O60716
GTEx:  ENSG00000198561 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60716
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
E-cadherin18Homo sapiensMutation(s): 0 
Gene Names: CDH1
UniProt & NIH Common Fund Data Resources
Find proteins for P12830 (Homo sapiens)
Explore P12830 
Go to UniProtKB:  P12830
PHAROS:  P12830
GTEx:  ENSG00000039068 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12830
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.234 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.201 (Depositor) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.403α = 90
b = 92.403β = 90
c = 171.89γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description