4NQQ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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 U S A 111: E4175-E4184

  • DOI: 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 ...

    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: 

    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.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cadherin-3A, B, C, D213Mus musculusMutation(s): 0 
Gene Names: Cdh3, Cdhp
UniProt
Find proteins for P10287 (Mus musculus)
Explore P10287 
Go to UniProtKB:  P10287
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10287
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU
Download Ideal Coordinates CCD File 
AA [auth D],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
AA [auth D],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
Z [auth D]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
R [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.085α = 90
b = 188.7β = 90
c = 53.15γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

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
  • Version 1.2: 2017-11-22
    Changes: Refinement description