6VEL

Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography.

Maker, A.Bolejack, M.Schecterson, L.Hammerson, B.Abendroth, J.Edwards, T.E.Staker, B.Myler, P.J.Gumbiner, B.M.

(2022) PNAS Nexus 1: pgac163-pgac163

  • DOI: https://doi.org/10.1093/pnasnexus/pgac163
  • Primary Citation of Related Structures:  
    6VEL, 7STZ

  • PubMed Abstract: 

    E-cadherin adhesion is regulated at the cell surface, a process that can be replicated by activating antibodies. We use cryo-electron microscopy (EM) and X-ray crystallography to examine functional states of the cadherin adhesive dimer. This dimer is mediated by N-terminal beta strand-swapping involving Trp2, and forms via a different transient X-dimer intermediate. X-dimers are observed in cryo-EM along with monomers and strand-swap dimers, indicating that X-dimers form stable interactions. A novel EC4-mediated dimer was also observed. Activating Fab binding caused no gross structural changes in E-cadherin monomers, but can facilitate strand swapping. Moreover, activating Fab binding is incompatible with the formation of the X-dimer. Both cryo-EM and X-ray crystallography reveal a distinctive twisted strand-swap dimer conformation caused by an outward shift in the N-terminal beta strand that may represent a strengthened state. Thus, regulation of adhesion involves changes in cadherin dimer configurations.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
66E8 Fab Heavy ChainA [auth H]243Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
66E8 Fab Light ChainB [auth L]233Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3,Cadherin-1331Saccharomyces cerevisiae S288CHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: SMT3YDR510WD9719.15CDH1CDHEUVO
UniProt & NIH Common Fund Data Resources
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
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 GroupsQ12306P12830
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.17α = 90
b = 142.17β = 90
c = 90.32γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 2.0: 2020-08-12
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-02-01
    Changes: Database references
  • Version 2.2: 2023-10-25
    Changes: Data collection, Refinement description