Skip to main content

 3K6D | pdb_00003k6d

Crystal structure of Xenopus laevis T-cadherin EC1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.285 (Depositor) 
  • R-Value Work: 
    0.227 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3K6D

This is version 1.2 of the entry. See complete history. 

Literature

T-cadherin structures reveal a novel adhesive binding mechanism

Ciatto, C., Bahna, F., Zampieri, N., Vansteenhouse, H.C., Katsamba, P.S., Ahlsen, G., Harrison, O.J., Brasch, J., Jin, X., Posy, S., Vendome, J., Ranscht, B., Jessell, T.M., Honig, B., Shapiro, L.

(2010) Nat Struct Mol Biol 17: 339-347

  • DOI: https://doi.org/10.1038/nsmb.1781
  • Primary Citation Related Structures: 
    3K5R, 3K5S, 3K6D, 3K6F, 3K6I

  • PubMed Abstract: 

    Vertebrate genomes encode 19 classical cadherins and about 100 nonclassical cadherins. Adhesion by classical cadherins depends on binding interactions in their N-terminal EC1 domains, which swap N-terminal beta-strands between partner molecules from apposing cells. However, strand-swapping sequence signatures are absent from nonclassical cadherins, raising the question of how these proteins function in adhesion. Here, we show that T-cadherin, a glycosylphosphatidylinositol (GPI)-anchored cadherin, forms dimers through an alternative nonswapped interface near the EC1-EC2 calcium-binding sites. Mutations within this interface ablate the adhesive capacity of T-cadherin. These nonadhesive T-cadherin mutants also lose the ability to regulate neurite outgrowth from T-cadherin-expressing neurons. Our findings reveal the likely molecular architecture of the T-cadherin homophilic interface and its requirement for axon outgrowth regulation. The adhesive binding mode used by T-cadherin may also be used by other nonclassical cadherins.


  • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 10.86 kDa 
  • Atom Count: 863 
  • Modeled Residue Count: 99 
  • Deposited Residue Count: 99 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
T-cadherin99Xenopus laevisMutation(s): 0 
Gene Names: cdh13, LOC495024
UniProt
Find proteins for Q5XHE3 (Xenopus laevis)
Explore Q5XHE3 
Go to UniProtKB:  Q5XHE3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XHE3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.285 (Depositor) 
  • R-Value Work:  0.227 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.91α = 90
b = 78.91β = 90
c = 62.577γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations