Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1

Experimental Data Snapshot

  • Resolution: 2.99 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Structural determinants of protocadherin-15 mechanics and function in hearing and balance perception.

Choudhary, D.Narui, Y.Neel, B.L.Wimalasena, L.N.Klanseck, C.F.De-la-Torre, P.Chen, C.Araya-Secchi, R.Tamilselvan, E.Sotomayor, M.

(2020) Proc Natl Acad Sci U S A 

  • DOI: https://doi.org/10.1073/pnas.1920444117
  • Primary Citation of Related Structures:  
    5TPK, 5ULY, 5W1D, 6BWN, 6BXU, 6E8F, 6EB5, 6EET, 6MFO, 6N22, 6N2E

  • PubMed Abstract: 

    The vertebrate inner ear, responsible for hearing and balance, is able to sense minute mechanical stimuli originating from an extraordinarily broad range of sound frequencies and intensities or from head movements. Integral to these processes is the tip-link protein complex, which conveys force to open the inner-ear transduction channels that mediate sensory perception. Protocadherin-15 and cadherin-23, two atypically large cadherins with 11 and 27 extracellular cadherin (EC) repeats, are involved in deafness and balance disorders and assemble as parallel homodimers that interact to form the tip link. Here we report the X-ray crystal structure of a protocadherin-15 + cadherin-23 heterotetrameric complex at 2.9-Å resolution, depicting a parallel homodimer of protocadherin-15 EC1-3 molecules forming an antiparallel complex with two cadherin-23 EC1-2 molecules. In addition, we report structures for 10 protocadherin-15 fragments used to build complete high-resolution models of the monomeric protocadherin-15 ectodomain. Molecular dynamics simulations and validated crystal contacts are used to propose models for the complete extracellular protocadherin-15 parallel homodimer and the tip-link bond. Steered molecular dynamics simulations of these models suggest conditions in which a structurally diverse and multimodal protocadherin-15 ectodomain can act as a stiff or soft gating spring. These results reveal the structural determinants of tip-link-mediated inner-ear sensory perception and elucidate protocadherin-15's structural and adhesive properties relevant in disease.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B [auth C],
C [auth B]
362Homo sapiensMutation(s): 0 
Gene Names: PCDH15USH1F
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QU1 (Homo sapiens)
Explore Q96QU1 
Go to UniProtKB:  Q96QU1
GTEx:  ENSG00000150275 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QU1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth C]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth C],
J [auth C],
K [auth C],
L [auth C],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.99 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.735α = 90
b = 95.906β = 90
c = 258.604γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

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 StatesR01 DC015271

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2020-10-07
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description