4NQQ

Crystal structure of mouse P-cadherin extracellular domains EC1-EC2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.USA 111: E4175-E4184

  • DOI: 10.1073/pnas.1416737111
  • Primary Citation of Related Structures:  

  • 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 heterophil ...

    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.,Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 hubbellw@jsei.ucla.edu lss8@columbia.edu bh6@columbia.edu.,Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Department of Systems Biology, Howard Hughes Medical Institute, Columbia University, New York, NY 10032; hubbellw@jsei.ucla.edu lss8@columbia.edu bh6@columbia.edu.,Department of Physics, University of Washington, Seattle, WA 98195; and.,Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Department of Systems Biology.,Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, New York, NY 10032;,Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Department of Systems Biology, Howard Hughes Medical Institute, Columbia University, New York, NY 10032;,Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Department of Systems Biology, hubbellw@jsei.ucla.edu lss8@columbia.edu bh6@columbia.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cadherin-3
A, B, C, D
213Mus musculusMutation(s): 0 
Gene Names: Cdh3 (Cdhp)
Find proteins for P10287 (Mus musculus)
Go to UniProtKB:  P10287
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 123.085α = 90.00
b = 188.700β = 90.00
c = 53.150γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MAR345data collection
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-10-22
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description