5ULU

Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with non-syndromic deafness (DFNB12) associated mutation D2148N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness.

Jaiganesh, A.De-la-Torre, P.Patel, A.A.Termine, D.J.Velez-Cortes, F.Chen, C.Sotomayor, M.

(2018) Structure 26: 1210

  • DOI: https://doi.org/10.1016/j.str.2018.06.003
  • Primary Citation of Related Structures:  
    5I8D, 5TFK, 5TFL, 5TFM, 5ULU, 5UN2, 5UZ8, 5VH2, 5VT8, 5VVM, 5W4T, 5WJ8, 5WJM

  • PubMed Abstract: 

    Cadherin-23 (CDH23) is an essential component of hair-cell tip links, fine filaments that mediate inner-ear mechanotransduction. The extracellular domain of CDH23 forms about three-fourths of the tip link with 27 extracellular cadherin (EC) repeats that are structurally similar but not identical to each other. Calcium (Ca 2+ ) coordination at the EC linker regions is key for tip-link elasticity and function. There are ∼116 sites in CDH23 affected by deafness-causing mutations, many of which alter conserved Ca 2+ -binding residues. Here we present crystal structures showing 18 CDH23 EC repeats, including the most and least conserved, a fragment carrying disease mutations, and EC repeats with non-canonical Ca 2+ -binding motif sequences and unusual secondary structure. Complementary experiments show deafness mutations' effects on stability and affinity for Ca 2+ . Additionally, a model of nine contiguous CDH23 EC repeats reveals helicity and potential parallel dimerization faces. Overall, our studies provide detailed structural insight into CDH23 function in mechanotransduction.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cadherin-23344Mus musculusMutation(s): 2 
Gene Names: Cdh23
UniProt & NIH Common Fund Data Resources
Find proteins for Q99PF4 (Mus musculus)
Explore Q99PF4 
Go to UniProtKB:  Q99PF4
IMPC:  MGI:1890219
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99PF4
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.238α = 90
b = 65.386β = 98.62
c = 114.651γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesDC012534
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesDC015271

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-05
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description