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- EMDB-75730: Protocadherin-15 extracellular domains 1-7 -

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Basic information

Entry
Database: EMDB / ID: EMD-75730
TitleProtocadherin-15 extracellular domains 1-7
Map dataPdch15 full map sharpened
Sample
  • Complex: Homodimer of protocadherin-15 extracellular domains 1-7
    • Protein or peptide: Protocadherin-15
KeywordsTip link / hearing / protocadherin / mechanosensation / CELL ADHESION
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsLiang X / Dillard L / Pathak R / Twomey EC / Muller U
Funding support United States, France, 6 items
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, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75730.png

Downloads & links

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Map

FileDownload / File: emd_75730.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPdch15 full map sharpened
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å		1.2 Å/pix.
x 360 pix.
= 432. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7977401 - 2.7394178
Average (Standard dev.)-0.00022121634 (±0.02518408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Pdch15 full map unsharpened

Fileemd_75730_additional_1.map
AnnotationPdch15 full map unsharpened
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Additional map: Pcdh15 EC3-5 local map half 1

Fileemd_75730_additional_10.map
AnnotationPcdh15 EC3-5 local map half 1
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Additional map: Pcdh15 EC3-5 local map half 2

Fileemd_75730_additional_11.map
AnnotationPcdh15 EC3-5 local map half 2
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Additional map: Pcdh15 EC6-7 local map sharpened

Fileemd_75730_additional_12.map
AnnotationPcdh15 EC6-7 local map sharpened
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Additional map: Pcdh15 EC6-7 local map unsharpened

Fileemd_75730_additional_13.map
AnnotationPcdh15 EC6-7 local map unsharpened
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Additional map: Pcdh15 EC6-7 local map half 1

Fileemd_75730_additional_14.map
AnnotationPcdh15 EC6-7 local map half 1
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Additional map: Composite map of local maps

Fileemd_75730_additional_2.map
AnnotationComposite map of local maps
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Additional map: Pcdh15 EC1-2 local map sharpened

Fileemd_75730_additional_3.map
AnnotationPcdh15 EC1-2 local map sharpened
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Additional map: Pcdh15 EC1-2 local map unsharpened

Fileemd_75730_additional_4.map
AnnotationPcdh15 EC1-2 local map unsharpened
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Additional map: Pcdh15 EC1-2 local map half 1

Fileemd_75730_additional_5.map
AnnotationPcdh15 EC1-2 local map half 1
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Additional map: Pcdh15 EC1-2 local map half 2

Fileemd_75730_additional_6.map
AnnotationPcdh15 EC1-2 local map half 2
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Additional map: Pcdh15 EC3-5 local map sharpened

Fileemd_75730_additional_7.map
AnnotationPcdh15 EC3-5 local map sharpened
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Additional map: Pcdh15 EC3-5 local map unsharpened

Fileemd_75730_additional_8.map
AnnotationPcdh15 EC3-5 local map unsharpened
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Additional map: Pcdh15 EC6-7 local map half 2

Fileemd_75730_additional_9.map
AnnotationPcdh15 EC6-7 local map half 2
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Half map: Pdch15 full map half 1

Fileemd_75730_half_map_1.map
AnnotationPdch15 full map half 1
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Half map: Pdch15 full map half 2

Fileemd_75730_half_map_2.map
AnnotationPdch15 full map half 2
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Sample components

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Entire : Homodimer of protocadherin-15 extracellular domains 1-7

EntireName: Homodimer of protocadherin-15 extracellular domains 1-7
Components
  • Complex: Homodimer of protocadherin-15 extracellular domains 1-7
    • Protein or peptide: Protocadherin-15

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Supramolecule #1: Homodimer of protocadherin-15 extracellular domains 1-7

SupramoleculeName: Homodimer of protocadherin-15 extracellular domains 1-7
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Protocadherin-15

MacromoleculeName: Protocadherin-15 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 87.829945 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YDDDWQYEDC KLARGGPPAT IVAIDEESRN GTILVDNMLI KGTAGGPDPT IELSLKDNVD YWVLLDPVKQ MLFLNSTGRV LDRDPPMNI HSIVVQVQCV NKKVGTVIYH EVRIVVRDRN DNSPTFKHES YYATVNELTP VGTTIFTGFS GDNGATDIDD G PNGQIEYV ...String:
YDDDWQYEDC KLARGGPPAT IVAIDEESRN GTILVDNMLI KGTAGGPDPT IELSLKDNVD YWVLLDPVKQ MLFLNSTGRV LDRDPPMNI HSIVVQVQCV NKKVGTVIYH EVRIVVRDRN DNSPTFKHES YYATVNELTP VGTTIFTGFS GDNGATDIDD G PNGQIEYV IQYNPEDPTS NDTFEIPLML TGNVVLRKRL NYEDKTRYYV IIQANDRAQN LNERRTTTTT LTVDVLDGDD LG PMFLPCV LVPNTRDCRP LTYQAAIPEL RTPEELNPIL VTPPIQAIDQ DRNIQPPSDR PGILYSILVG TPEDYPRFFH MHP RTAELT LLEPVNRDFH QKFDLVIKAE QDNGHPLPAF ASLHIEILDE NNQSPYFTMP SYQGYILESA PVGATISESL NLTT PLRIV ALDKDIEDTK DPELHLFLND YTSVFTVTPT GITRYLTLLQ PVDREEQQTY TFLITAFDGV QESEPVVVNI RVMDA NDNT PTFPEISYDV YVYTDMSPGD SVIQLTAVDA DEGSNGEISY EILVGGKGDF VINKTTGLVS IAPGVELIVG QTYALT VQA SDNAPPAERR HSICTVYIEV LPPNNQSPPR FPQLMYSLEV SEAMRIGAIL LNLQATDREG DPITYAIENG DPQRVFN LS ETTGILSLGK ALDRESTDRY ILIVTASDGR PDGTSTATVN IVVTDVNDNA PVFDPYLPRN LSVVEEEANA FVGQVRAT D PDAGINGQVH YSLGNFNNLF RITSNGSIYT AVKLNREARD HYELVVVATD GAVHPRHSTL TLYIKVLDI

UniProtKB: Protocadherin-15

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 151796
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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