Crystal structure of mouse N-cadherin EC1-2 with AA insertion between residues 2 and 3

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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Structural and energetic determinants of adhesive binding specificity in type I cadherins.

Vendome, J.Felsovalyi, K.Song, H.Yang, Z.Jin, X.Brasch, J.Harrison, O.J.Ahlsen, G.Bahna, F.Kaczynska, A.Katsamba, P.S.Edmond, D.Hubbell, W.L.Shapiro, L.Honig, B.

(2014) Proc Natl Acad Sci U S A 111: E4175-E4184

  • DOI: https://doi.org/10.1073/pnas.1416737111
  • Primary Citation of Related Structures:  
    4NQQ, 4NUM, 4NUP, 4NUQ

  • PubMed Abstract: 

    Type I cadherin cell-adhesion proteins are similar in sequence and structure and yet are different enough to mediate highly specific cell-cell recognition phenomena. It has previously been shown that small differences in the homophilic and heterophilic binding affinities of different type I family members can account for the differential cell-sorting behavior. Here we use a combination of X-ray crystallography, analytical ultracentrifugation, surface plasmon resonance and double electron-electron resonance (DEER) electron paramagnetic resonance spectroscopy to identify the molecular determinants of type I cadherin dimerization affinities. Small changes in sequence are found to produce subtle structural and dynamical changes that impact relative affinities, in part via electrostatic and hydrophobic interactions, and in part through entropic effects because of increased conformational heterogeneity in the bound states as revealed by DEER distance mapping in the dimers. These findings highlight the remarkable ability of evolution to exploit a wide range of molecular properties to produce closely related members of the same protein family that have affinity differences finely tuned to mediate their biological roles.

  • Organizational Affiliation

    Jules Stein Eye Institute and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
217Mus musculusMutation(s): 0 
Gene Names: Cdh2
Find proteins for P15116 (Mus musculus)
Explore P15116 
Go to UniProtKB:  P15116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15116
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.504α = 90
b = 65.791β = 90
c = 102.505γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2014-09-24 
  • Deposition Author(s): Jin, X.

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references