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- PDB-9dfs: Structure of novel Myo7a-N isoform (ADP-bound) expressed in senso... -

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Basic information

Entry
Database: PDB / ID: 9dfs
TitleStructure of novel Myo7a-N isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains), bound to F-actin
Components
  • Actin, alpha skeletal muscle
  • Unconventional myosin-VIIa
KeywordsMOTOR PROTEIN / actomyosin / hair cells
Function / homology
Function and homology information


mechanoreceptor differentiation / pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / phagolysosome assembly / inner ear receptor cell differentiation / equilibrioception ...mechanoreceptor differentiation / pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / phagolysosome assembly / inner ear receptor cell differentiation / equilibrioception / inner ear receptor cell stereocilium organization / sensory perception of light stimulus / photoreceptor connecting cilium / inner ear auditory receptor cell differentiation / sensory organ development / actin filament-based movement / auditory receptor cell stereocilium organization / stereocilium / inner ear morphogenesis / myosin complex / lysosome organization / microfilament motor activity / cytoskeletal motor activator activity / sensory perception / inner ear development / spectrin binding / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / microvillus / mesenchyme migration / cytoskeletal motor activity / skeletal muscle myofibril / phagocytosis / cochlea development / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / actin monomer binding / photoreceptor outer segment / visual perception / skeletal muscle fiber development / sensory perception of sound / actin filament polymerization / stress fiber / titin binding / photoreceptor inner segment / filopodium / actin filament / intracellular protein transport / endocytosis / ADP binding / intracellular protein localization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / melanosome / lamellipodium / actin binding / cell body / cell cortex / calmodulin binding / apical plasma membrane / protein domain specific binding / lysosomal membrane / positive regulation of gene expression / calcium ion binding / synapse / protein-containing complex binding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / Myosin VII N-terminal beta barrel domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain ...: / Myosin VII N-terminal beta barrel domain / Class VII myosin, motor domain / Myosin VII, FERM domain C-lobe, repeat 1 / Myosin VII, FERM domain C-lobe, repeat 2 / Myosin-X FERM PH domain-like / : / MyTH4 domain / MyTH4 domain superfamily / MyTH4 domain / MyTH4 domain profile. / Domain in Myosin and Kinesin Tails / RA like domain / IRS-type PTB domain / PTB domain (IRS-1 type) / IQ calmodulin-binding motif / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Kinesin motor domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / ATPase, nucleotide binding domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle / Unconventional myosin-VIIa
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsEgelman, E.H. / Shin, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Nat Commun / Year: 2026
Title: Tonotopic specialization of MYO7A isoforms in auditory hair cells.
Authors: Sihan Li / Jinho Park / Tobey M Phan / Giusy A Caprara / Natchanon Sittipongpittaya / Gloria M Sheynkman / Anthony W Peng / Edward H Egelman / Jonathan E Bird / Jung-Bum Shin /
Abstract: Mutations in Myo7a cause Usher syndrome type 1B and non-syndromic deafness, but the precise function of MYO7A in sensory hair cells remains unclear. Using long-read sequencing, we identify and ...Mutations in Myo7a cause Usher syndrome type 1B and non-syndromic deafness, but the precise function of MYO7A in sensory hair cells remains unclear. Using long-read sequencing, we identify and characterize a novel isoform, MYO7A-N, expressed in auditory hair cells alongside the canonical MYO7A-C. Isoform-specific knock-in mouse models reveal that inner hair cells primarily express MYO7A-C, while outer hair cells express both isoforms in opposing tonotopic gradients. Both isoforms are localized to the upper tip-link insertion site, consistent with a role in the tip link for mechanotransduction. Loss of MYO7A-N leads to outer hair cell degeneration and progressive hearing loss. Cryo-EM structures reveal isoform-specific differences at actomyosin interfaces, correlating with distinct ATPase activities. These findings reveal an unexpected layer of molecular diversity within the mechanotransduction machinery. We propose that MYO7A isoform specialization enables fine-tuning of tip-link tension, thus hearing sensitivity, and contributes to the frequency-resolving power of the cochlea.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Unconventional myosin-VIIa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,94512
Polymers249,1394
Non-polymers1,8068
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 Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / Gene: ACTA1, ACTA / Production host: Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Unconventional myosin-VIIa


Mass: 122808.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Myo7a-N isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo7a, Myo7 / Production host: unidentified baculovirus / References: UniProt: P97479
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: actomyosin / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.8
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0 ° / Axial rise/subunit: 0.001 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 878646 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214760
ELECTRON MICROSCOPYf_angle_d0.55220013
ELECTRON MICROSCOPYf_dihedral_angle_d8.3492036
ELECTRON MICROSCOPYf_chiral_restr0.0422209
ELECTRON MICROSCOPYf_plane_restr0.0042578

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