6VEL | pdb_00006vel

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 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6VEL

This is version 2.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 89.54 kDa 
  • Atom Count: 4,889 
  • Modeled Residue Count: 630 
  • Deposited Residue Count: 807 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
66E8 Fab Heavy ChainA [auth H]243Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
66E8 Fab Light ChainB [auth L]233Mus musculusMutation(s): 0 
Find similar proteins by:|  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 P12830 (Homo sapiens)
Explore P12830 
Go to UniProtKB:  P12830
PHAROS:  P12830
GTEx:  ENSG00000039068 
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ12306P12830
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth H]
E [auth H]
F [auth L]
G [auth L]
J [auth C]
D [auth H],
E [auth H],
F [auth L],
G [auth L],
J [auth C],
K [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
H [auth C],
I [auth C],
L [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.236 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 31 2 1
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 

Deposition Data

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
  • Version 2.3: 2024-10-09
    Changes: Structure summary
  • Version 2.4: 2025-10-22
    Changes: Structure summary