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- EMDB-46819: Structure of canonical Myo7a-C isoform (ADP-bound) expressed in s... -

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Basic information

Entry
Database: EMDB / ID: EMD-46819
TitleStructure of canonical Myo7a-C isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains), bound to F-actin
Map data
Sample
  • Complex: Actin with canonical Myo7a-C isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains)
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Unconventional myosin-VIIa
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordshair cells / actin / actomyosin / MOTOR PROTEIN
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
Actin, alpha skeletal muscle / Unconventional myosin-VIIa
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Mus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsEgelman EH / Shin JB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: To Be Published
Title: Structure of canonical Myo7a-C isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains), bound to F-actin
Authors: Egelman EH / Shin JB
History
DepositionAug 30, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46819.png

Downloads & links

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Map

FileDownload / File: emd_46819.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 512 pix.
= 552.96 Å		1.08 Å/pix.
x 512 pix.
= 552.96 Å		1.08 Å/pix.
x 512 pix.
= 552.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.8029499 - 1.6886885
Average (Standard dev.)0.00031820947 (±0.039072916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 552.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46819_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46819_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Actin with canonical Myo7a-C isoform (ADP-bound) expressed in sen...

EntireName: Actin with canonical Myo7a-C isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains)
Components
  • Complex: Actin with canonical Myo7a-C isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains)
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Unconventional myosin-VIIa
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Actin with canonical Myo7a-C isoform (ADP-bound) expressed in sen...

SupramoleculeName: Actin with canonical Myo7a-C isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Unconventional myosin-VIIa

MacromoleculeName: Unconventional myosin-VIIa / type: protein_or_peptide / ID: 2
Details: Myo7a-C isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 76.781516 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: LQKGDYVWMD LKSGQEFDVP IGAVVKLCDS GQIQAVDDED NEHWISPQNA THIKPMHPTS VHGVEDMIRL GDLNEAGILR NLLIRYRDH LIYTYTGSIL VAVNPYQLLS IYSPEHIRQY TNKKIGEMPP HIFAIADNCY FNMKRNNRDQ CCIISGESGA G KTESTKLI ...String:
LQKGDYVWMD LKSGQEFDVP IGAVVKLCDS GQIQAVDDED NEHWISPQNA THIKPMHPTS VHGVEDMIRL GDLNEAGILR NLLIRYRDH LIYTYTGSIL VAVNPYQLLS IYSPEHIRQY TNKKIGEMPP HIFAIADNCY FNMKRNNRDQ CCIISGESGA G KTESTKLI LQFLAAISGQ HSWIEQQVLE ATPILEAFGN AKTIRNDNSS RFGKYIDIHF NKRGAIEGAK IEQYLLEKSR VC RQAPDER NYHVFYCMLE GMNEEEKKKL GLGQAADYNY LAMGNCITCE GRVDSQEYAN IRSAMKVLMF TDTENWEISK LLA AILHMG NLQYEARTFE NLDACEVLFS PSLATAASLL EVNPPDLMSC LTSRTLITRG ETVSTPLSRE QALDVRDAFV KGIY GRLFV WIVEKINAAI YKPPPLEVKN SRRSIGLLDI FGFENFTVNS FEQLCINFAN EHLQQFFVRH VFKLEQEEYD LESID WLHI EFTDNQEALD MIANRPMNVI SLIDEESKFP KGTDATMLHK LNSQHKLNAN YVPPKNSHET QFGINHFAGV VYYESQ GFL EKNRDTLHGD IIQLVHSSRN KFIKQIFQAD VAMGAETRKR SPTLSSQFKR SLELLMRTLG ACQPFFVRCI KPNEFKK PM LFDRHLCVRQ LRYSGMMETI RIRHAGYP

UniProtKB: Unconventional myosin-VIIa

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.8
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 99 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 0.01 Å
Applied symmetry - Helical parameters - Δ&Phi: 0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 447188
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 1725905
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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