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- EMDB-46818: Structure of novel Myo7a-N isoform (ADP-bound) expressed in senso... -

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Basic information

Entry
Database: EMDB / ID: EMD-46818
TitleStructure of novel Myo7a-N isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains), bound to F-actin
Map data
Sample
  • Complex: actomyosin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Unconventional myosin-VIIa
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactomyosin / hair cells / 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 / cell projection organization / stereocilium / auditory receptor cell stereocilium organization / cytoskeletal motor activator activity / lysosome organization / inner ear morphogenesis / myosin heavy chain binding / microfilament motor activity / spectrin binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / microvillus / inner ear development / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / cochlea development / actin monomer binding / photoreceptor outer segment / phagocytosis / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / photoreceptor inner segment / visual perception / actin filament / filopodium / 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 / apical plasma membrane / hydrolase activity / protein domain specific binding / lysosomal membrane / calcium ion binding / synapse / positive regulation of gene expression / magnesium ion binding / 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 / 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 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
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 novel Myo7a-N isoform (ADP-bound) expressed in sensory hair cells (head domain + first two IQ domains), bound to F-actin
Authors: Egelman EH
History
DepositionAug 30, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46818.png

Downloads & links

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Map

FileDownload / File: emd_46818.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: 0.32
Minimum - Maximum-2.4983904 - 3.1987302
Average (Standard dev.)0.0010614132 (±0.04259729)
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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Additional map: #1

Fileemd_46818_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46818_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46818_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : actomyosin

EntireName: actomyosin
Components
  • Complex: actomyosin
    • 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: actomyosin

SupramoleculeName: actomyosin / 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) / Tissue: skeletal muscle
Molecular weightTheoretical: 42.109973 KDa
Recombinant expressionOrganism: Oryctolagus cuniculus (rabbit)
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-N 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: 122.808883 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: GNKAGMESPG SPADPGEAPA PPPGKWALVR NLNQTLKTFA VLPGDYVWMD LKSGQEFDVP IGAVVKLCDS GQIQVVDDED NEHWISPQN ATHIKPMHPT SVHGVEDMIR LGDLNEAGIL RNLLIRYRDH LIYTYTGSIL VAVNPYQLLS IYSPEHIRQY T NKKIGEMP ...String:
GNKAGMESPG SPADPGEAPA PPPGKWALVR NLNQTLKTFA VLPGDYVWMD LKSGQEFDVP IGAVVKLCDS GQIQVVDDED NEHWISPQN ATHIKPMHPT SVHGVEDMIR LGDLNEAGIL RNLLIRYRDH LIYTYTGSIL VAVNPYQLLS IYSPEHIRQY T NKKIGEMP PHIFAIADNC YFNMKRNNRD QCCIISGESG AGKTESTKLI LQFLAAISGQ HSWIEQQVLE ATPILEAFGN AK TIRNDNS SRFGKYIDIH FNKRGAIEGA KIEQYLLEKS RVCRQAPDER NYHVFYCMLE GMNEEEKKKL GLGQAADYNY LAM GNCITC EGRVDSQEYA NIRSAMKVLM FTDTENWEIS KLLAAILHMG NLQYEARTFE NLDACEVLFS PSLATAASLL EVNP PDLMS CLTSRTLITR GETVSTPLSR EQALDVRDAF VKGIYGRLFV WIVEKINAAI YKPPPLEVKN SRRSIGLLDI FGFEN FTVN SFEQLCINFA NEHLQQFFVR HVFKLEQEEY DLESIDWLHI EFTDNQEALD MIANRPMNVI SLIDEESKFP KGTDAT MLH KLNSQHKLNA NYVPPKNSHE TQFGINHFAG VVYYESQGFL EKNRDTLHGD IIQLVHSSRN KFIKQIFQAD VAMGAET RK RSPTLSSQFK RSLELLMRTL GACQPFFVRC IKPNEFKKPM LFDRHLCVRQ LRYSGMMETI RIRHAGYPIR YSFVEFVE R YRVLLPGVKP AYKQGDLRGT CQRMAEAVLG THDDWQIGKT KIFLKDHHDM LLEVERDKAI TDRVILLQKV IRGFKDRSN FLRLKSAATL IQRHWRGHHC RKNYEGSMVS KGEELFTGVV PILVELDGDV NGHKFSVSGE GEGDATYGKL TLKFICTTGK LPVPWPTLV TTLTYGVQCF SRYPDHMKQH DFFKSAMPEG YVQERTIFFK DDGNYKTRAE VKFEGDTLVN RIELKGIDFK E DGNILGHK LEYNYNSHNV YIMADKQKNG IKVNFKIRHN IEDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSALSKD PN EKRDHMV LLEFVTAAGI TLGMDELYKA AADYKDDDDK

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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 0.001 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.0 °
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: 878646
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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