Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.34 kDa 
• Atom Count: 1877 
• Residue Count: 213 
• Unique protein chains: 1

2O72

Crystal Structure Analysis of human E-cadherin (1-213)

• DOI: 10.2210/pdb2O72/pdb

• Classification: CELL ADHESION, METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-09 Released: 2007-10-09 
• Deposition Author(s): Parisini, E., Wang, J.-H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

The Crystal Structure of Human E-cadherin Domains 1 and 2, and Comparison with other Cadherins in the Context of Adhesion Mechanism

Parisini, E., Higgins, J.M.G., Liu, J.-H., Brenner, M.B., Wang, J.-H.

(2007) J Mol Biol 373: 401-411

• PubMed: 17850815 
• DOI: 10.1016/j.jmb.2007.08.011
• Primary Citation of Related Structures:  
  2O72


• PubMed Abstract: 
  

Cell adhesion mediated by type I cadherins involves homophilic "trans" interactions that are thought to be brought about by a strand exchange mechanism involving the N-terminal extracellular domain. Here, we present the high-resolution crystal structure of the N-terminal two domains of human E-cadherin. Comparison of this structure with other type I cadherin structures reveals features that are likely to be critical to facilitate dimerization by strand exchange as well as dimer flexibility. We integrate this structural knowledge to provide a model for type I cadherin adhesive interactions. Intra-molecular docking of the conserved N-terminal "adhesion arm" into the acceptor pocket in monomeric E-cadherin appears largely identical to inter-molecular docking of the adhesion arm in adhesive trans dimers. A strained conformation of the adhesion arm in the monomer, however, may create an equilibrium between "open" and "closed" forms that primes the cadherin for formation of adhesive interactions, which are then stabilized by additional dimer-specific contacts. By contrast, in type II cadherins, strain in the adhesion arm appears absent and a much larger surface area is involved in trans adhesion, which may compensate the activation energy required to peel off the intra-molecularly docked arm. It seems that evolution has selected slightly different adhesion mechanisms for type I and type II cadherins.

---

Organizational Affiliation: 

Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epithelial-cadherin	A	213	Homo sapiens	Mutation(s): 1  Gene Names: CDH1, CDHE, UVO
Find proteins for P12830 (Homo sapiens) Explore P12830  Go to UniProtKB:  P12830
NIH Common Fund Data Resources
PHAROS  P12830 GTEx  ENSG00000039068

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.234 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.341	α = 90
b = 41.077	β = 111.15
c = 59.542	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-09 
• Released Date: 2007-10-09 
Deposition Author(s): Parisini, E., Wang, J.-H.

Revision History 

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description