3MVS

Structure of the N-terminus of Cadherin 23

• PDB DOI:  https://doi.org/10.2210/pdb3MVS/pdb

• Classification: CELL ADHESION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-05-04 Released: 2010-06-09 
• Deposition Author(s): Clark, P., Joseph, J.S., Kolatkar, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.188 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Structure of the N terminus of cadherin 23 reveals a new adhesion mechanism for a subset of cadherin superfamily members.

Elledge, H.M., Kazmierczak, P., Clark, P., Joseph, J.S., Kolatkar, A., Kuhn, P., Muller, U.

(2010) Proc Natl Acad Sci U S A 107: 10708-10712

• PubMed: 20498078 
• DOI: https://doi.org/10.1073/pnas.1006284107
• Primary Citation of Related Structures:  
  3MVS


• PubMed Abstract: 
  

The cadherin superfamily encodes more than 100 receptors with diverse functions in tissue development and homeostasis. Classical cadherins mediate adhesion by binding interactions that depend on their N-terminal extracellular cadherin (EC) domains, which swap N-terminal beta-strands. Sequence alignments suggest that the strand-swap binding mode is not commonly used by functionally divergent cadherins. Here, we have determined the structure of the EC1-EC2 domains of cadherin 23 (CDH23), which binds to protocadherin 15 (PCDH15) to form tip links of mechanosensory hair cells. Unlike classical cadherins, the CDH23 N terminus contains polar amino acids that bind Ca(2+). The N terminus of PCDH15 also contains polar amino acids. Mutations in polar amino acids within EC1 of CDH23 and PCDH15 abolish interaction between the two cadherins. PCDH21 and PCDH24 contain similarly charged N termini, suggesting that a subset of cadherins share a common interaction mechanism that differs from the strand-swap binding mode of classical cadherins.

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Organizational Affiliation: 

Department of Cell Biology and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.88 kDa 
• Atom Count: 2,036 
• Modelled Residue Count: 210 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-23	A	210	Mus musculus	Mutation(s): 0  Gene Names: Cdh23
UniProt & NIH Common Fund Data Resources
Find proteins for Q99PF4 (Mus musculus) Explore Q99PF4  Go to UniProtKB:  Q99PF4
IMPC:  MGI:1890219

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	AA [auth A], BA [auth A], CA [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], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.188 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.375	α = 90
b = 64.208	β = 110.89
c = 47.859	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Clark, P., Joseph, J.S., Kolatkar, A.R.

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance