3UBG

Crystal structure of Drosophila N-cadherin EC1-3, II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca2+-free interdomain linkers.

Jin, X.Walker, M.A.Felsovalyi, K.Vendome, J.Bahna, F.Mannepalli, S.Cosmanescu, F.Ahlsen, G.Honig, B.Shapiro, L.

(2012) Proc Natl Acad Sci U S A 109: E127-E134

  • DOI: 10.1073/pnas.1117538108
  • Primary Citation of Related Structures:  
    3UBH, 3UBF, 3UBG

  • PubMed Abstract: 
  • Vertebrate classical cadherins mediate selective calcium-dependent cell adhesion by mechanisms now understood at the atomic level. However, structures and adhesion mechanisms of cadherins from invertebrates, which are highly divergent yet function in ...

    Vertebrate classical cadherins mediate selective calcium-dependent cell adhesion by mechanisms now understood at the atomic level. However, structures and adhesion mechanisms of cadherins from invertebrates, which are highly divergent yet function in similar roles, remain unknown. Here we present crystal structures of three- and four-tandem extracellular cadherin (EC) domain segments from Drosophila N-cadherin (DN-cadherin), each including the predicted N-terminal EC1 domain (denoted EC1') of the mature protein. While the linker regions for the EC1'-EC2' and EC3'-EC4' pairs display binding of three Ca(2+) ions similar to that of vertebrate cadherins, domains EC2' and EC3' are joined in a "kinked" orientation by a previously uncharacterized Ca(2+)-free linker. Biophysical analysis demonstrates that a construct containing the predicted N-terminal nine EC domains of DN-cadherin forms homodimers with affinity similar to vertebrate classical cadherins, whereas deleting the ninth EC domain ablates dimerization. These results suggest that, unlike their vertebrate counterparts, invertebrate cadherins may utilize multiple EC domains to form intercellular adhesive bonds. Sequence analysis reveals that similar Ca(2+)-free linkers are widely distributed in the ectodomains of both vertebrate and invertebrate cadherins.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neural-cadherinA, B316Drosophila melanogasterMutation(s): 0 
Gene Names: CadNCG7100
Find proteins for O15943 (Drosophila melanogaster)
Explore O15943 
Go to UniProtKB:  O15943
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.218α = 90
b = 113.769β = 123.57
c = 87.872γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2012-01-18
    Changes: Database references
  • Version 1.2: 2013-06-26
    Changes: Database references
  • Version 1.3: 2014-11-12
    Changes: Structure summary
  • Version 1.4: 2017-11-08
    Changes: Refinement description