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: 46.53 kDa 
• Atom Count: 3359 
• Residue Count: 418 
• Unique protein chains: 1

3LNH

Crystal structure of E-cadherin EC12 W2A

• DOI: 10.2210/pdb3LNH/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-02-02 Released: 2010-03-02 
• Deposition Author(s): Harrison, O., Jin, X., Shapiro, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

Two-step adhesive binding by classical cadherins.

Harrison, O.J., Bahna, F., Katsamba, P.S., Jin, X., Brasch, J., Vendome, J., Ahlsen, G., Carroll, K.J., Price, S.R., Honig, B., Shapiro, L.

(2010) Nat Struct Mol Biol 17: 348-357

• PubMed: 20190754 
• DOI: 10.1038/nsmb.1784
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Crystal structures of classical cadherins have revealed two dimeric configurations. In the first, N-terminal beta-strands of EC1 domains 'swap' between partner molecules. The second configuration (the 'X dimer'), also observed for T-cadherin, is mediated by residues near the EC1-EC2 calcium binding sites, and N-terminal beta-strands of partner EC1 domains, though held adjacent, do not swap. Here we show that strand-swapping mutants of type I and II classical cadherins form X dimers. Mutant cadherins impaired for X-dimer formation show no binding in short-time frame surface plasmon resonance assays, but in long-time frame experiments, they have homophilic binding affinities close to that of wild type. Further experiments show that exchange between monomers and dimers is slowed in these mutants. These results reconcile apparently disparate results from prior structural studies and suggest that X dimers are binding intermediates that facilitate the formation of strand-swapped dimers.

---

Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cadherin-1	A, B	213	Mus musculus	Mutation(s): 1  Gene Names: Cdh1
Find proteins for P09803 (Mus musculus) Explore P09803  Go to UniProtKB:  P09803
NIH Common Fund Data Resources
IMPC  MGI:88354

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.536	α = 90
b = 80.857	β = 116.84
c = 72.519	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-02 
• Released Date: 2010-03-02 
Deposition Author(s): Harrison, O., Jin, X., Shapiro, L.

Revision History 

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance