6VEL image
Deposition Date 2020-01-02
Release Date 2020-01-29
Last Version Date 2025-10-22
Entry Detail
PDB ID:
6VEL
Title:
Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.65 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 31 2 1
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-like protein SMT3,Cadherin-1
Gene (Uniprot):CDH1, SMT3
Chain IDs:C
Chain Length:331
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Polymer Type:polypeptide(L)
Molecule:66E8 Fab Heavy Chain
Chain IDs:A (auth: H)
Chain Length:243
Number of Molecules:1
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:66E8 Fab Light Chain
Chain IDs:B (auth: L)
Chain Length:233
Number of Molecules:1
Biological Source:Mus musculus
Primary Citation
Regulation of multiple dimeric states of E-cadherin by adhesion activating antibodies revealed through Cryo-EM and X-ray crystallography.
Pnas Nexus 1 pgac163 pgac163 (2022)
PMID: 36157596 DOI: 10.1093/pnasnexus/pgac163

Abstact

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.

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