3LNH

Crystal structure of E-cadherin EC12 W2A


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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cadherin-1A, B213Mus musculusMutation(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
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 = 120.536α = 90
b = 80.857β = 116.84
c = 72.519γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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