5UZ8 | pdb_00005uz8

Crystal Structure of Mouse Cadherin-23 EC22-24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.188 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 37.23 kDa 
  • Atom Count: 3,098 
  • Modeled Residue Count: 317 
  • Deposited Residue Count: 334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cadherin-23334Mus musculusMutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99PF4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH

Query on GSH



Download:Ideal Coordinates CCD File
L [auth A]Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.188 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.537α = 90
b = 57.208β = 112.55
c = 114.667γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesR00 DC012534
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesR01 DC015271

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-19
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description