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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


pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus ...pigment granule localization / pigment granule transport / upper tip-link density / The canonical retinoid cycle in rods (twilight vision) / myosin VII complex / stereocilium base / inner ear receptor cell differentiation / phagolysosome assembly / equilibrioception / sensory perception of light stimulus / mechanoreceptor differentiation / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / inner ear auditory receptor cell differentiation / actin filament-based movement / sensory perception / stereocilium / cell projection organization / auditory receptor cell stereocilium organization / cytoskeletal motor activator activity / lysosome organization / inner ear morphogenesis / spectrin binding / myosin heavy chain binding / microfilament motor activity / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / microvillus / mesenchyme migration / inner ear development / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / cochlea development / photoreceptor outer segment / phagocytosis / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / photoreceptor inner segment / visual perception / filopodium / actin filament / intracellular protein transport / sensory perception of sound / ADP binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / intracellular protein localization / melanosome / lamellipodium / cell body / cell cortex / calmodulin binding / hydrolase activity / apical plasma membrane / protein domain specific binding / lysosomal membrane / calcium ion binding / synapse / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
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 / MyTH4 domain profile. ...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 central domain / FERM/acyl-CoA-binding protein superfamily / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / 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: To Be Published
Title: Structure of novel Myo7a-N isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains), bound to F-actin
Authors: Egelman, E.H.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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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