3UBF

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

• PDB DOI:  https://doi.org/10.2210/pdb3UBF/pdb

• Classification: CELL ADHESION
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-24 Released: 2011-12-21 
• Deposition Author(s): Jin, X., Walker, M.A., Shapiro, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 

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

• PubMed: 22171007 
• DOI: https://doi.org/10.1073/pnas.1117538108
• Primary Citation of Related Structures:  
  3UBF, 3UBG, 3UBH


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.15 kDa 
• Atom Count: 2,533 
• Modelled Residue Count: 298 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neural-cadherin	A	316	Drosophila melanogaster	Mutation(s): 0  Gene Names: CadN, CG7100
UniProt
Find proteins for O15943 (Drosophila melanogaster) Explore O15943  Go to UniProtKB:  O15943

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	T [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.279 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.289	α = 90
b = 96.289	β = 90
c = 148.196	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Jin, X., Walker, M.A., Shapiro, L.

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
• Version 1.5: 2019-07-17
  Changes: Data collection, Refinement description