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- PDB-11iy: Protocadherin-15 extracellular domains 1-7 -

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Basic information

Entry
Database: PDB / ID: 11iy
TitleProtocadherin-15 extracellular domains 1-7
ComponentsProtocadherin-15
KeywordsCELL ADHESION / Tip link / hearing / protocadherin / mechanosensation
Function / homology
Function and homology information


detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / photoreceptor cell maintenance ...detection of mechanical stimulus involved in equilibrioception / equilibrioception / sensory perception of light stimulus / inner ear receptor cell stereocilium organization / righting reflex / inner ear auditory receptor cell differentiation / stereocilium bundle / detection of mechanical stimulus involved in sensory perception of sound / stereocilium / photoreceptor cell maintenance / non-motile cilium assembly / auditory receptor cell stereocilium organization / adult walking behavior / homophilic cell-cell adhesion / inner ear development / startle response / actin filament bundle assembly / photoreceptor outer segment / visual perception / cell adhesion molecule binding / morphogenesis of an epithelium / actin filament organization / locomotory behavior / sensory perception of sound / response to calcium ion / multicellular organism growth / cell adhesion / calcium ion binding / synapse / : / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...: / PCDH15-like domain / Protocadherin-15 / Extracellular cadherin domain / Extracellular Cadherin domain / : / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsLiang, X. / Dillard, L. / Pathak, R. / Twomey, E.C. / Muller, U.
Funding support United States, France, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154904 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM157915 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)RO1DC005965 United States
Other privateFPA RD-2024-1 France
Other private United States
Other private United States
CitationJournal: bioRxiv / Year: 2026
Title: Cryo-EM reveals a right-handed double-helix dimer architecture of PCDH15 critical for mechanotransduction.
Authors: Xiaoping Liang / Roshan Pathak / Xufeng Qiu / Lucas Dillard / Edward C Twomey / Ulrich Müller
Abstract: Tip links connect the stereocilia of mechanosensory hair cells in the inner ear and transmit force onto mechanotransduction (MET) channels. Tip links consist of protocadherin 15 (PCDH15) and cadherin ...Tip links connect the stereocilia of mechanosensory hair cells in the inner ear and transmit force onto mechanotransduction (MET) channels. Tip links consist of protocadherin 15 (PCDH15) and cadherin 23 (CDH23), which assemble into an extracellular filament approximately 150 nm in length. Rare freeze-etched electron microscopy (EM) images have suggested that tip links could be right-handed double helices in vivo, but direct structural evidence has been lacking. Using cryo-EM we determined the structure of a large part of the extracellular PCDH15 domain. Two PCDH15 molecules form a parallel cis dimer stabilized by several dimerization interfaces, including two strand crossovers and two parallel contacts, yielding a right-handed double helix. Functional studies show that mutations in PCDH15 dimerization-domains impair MET. Our results establish the molecular foundation for how PCDH15 forms a right-handed double helix to enable mechanical sensing.
History
DepositionFeb 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Protocadherin-15
D: Protocadherin-15


Theoretical massNumber of molelcules
Total (without water)175,6602
Polymers175,6602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protocadherin-15


Mass: 87829.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pcdh15 / Production host: Homo sapiens (human) / References: UniProt: Q99PJ1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homodimer of protocadherin-15 extracellular domains 1-7
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151796 / Symmetry type: POINT
RefinementHighest resolution: 3.57 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212636
ELECTRON MICROSCOPYf_angle_d0.66117302
ELECTRON MICROSCOPYf_dihedral_angle_d8.7661728
ELECTRON MICROSCOPYf_chiral_restr0.0482018
ELECTRON MICROSCOPYf_plane_restr0.0072306

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