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- EMDB-60122: Human left ventricle actin and myosin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60122
TitleHuman left ventricle actin and myosin complex
Map data
Sample
  • Organelle or cellular component: human left ventricle actin and myosin complex
    • Protein or peptide: Myosin-7
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsprotein binding / actin / myosin
Function / homology
Function and homology information


regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / actin filament-based movement / actin-myosin filament sliding / muscle myosin complex / cardiac myofibril assembly / regulation of the force of heart contraction / Formation of the dystrophin-glycoprotein complex (DGC) / transition between fast and slow fiber / myosin filament ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / actin filament-based movement / actin-myosin filament sliding / muscle myosin complex / cardiac myofibril assembly / regulation of the force of heart contraction / Formation of the dystrophin-glycoprotein complex (DGC) / transition between fast and slow fiber / myosin filament / adult heart development / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / actomyosin structure organization / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex / myosin II complex / I band / RHOB GTPase cycle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / heart contraction / myosin binding / myofibril / mesenchyme migration / skeletal muscle thin filament assembly / RHOA GTPase cycle / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / cardiac muscle contraction / stress fiber / regulation of heart rate / muscle contraction / actin filament organization / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Z disc / actin filament binding / lamellipodium / actin cytoskeleton / cell body / response to ethanol / blood microparticle / calmodulin binding / hydrolase activity / response to xenobiotic stimulus / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / extracellular space / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin motor domain profile. ...DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / 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. / 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 / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin-7 / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLi DN / Zhao QY / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human left ventricle actin and myosin complex
Authors: Li DN / Zhao QY / Liu C
History
DepositionMay 13, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60122.png

Downloads & links

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Map

FileDownload / File: emd_60122.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.025849605 - 0.06291188
Average (Standard dev.)0.00003678643 (±0.00082286884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60122_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_60122_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 : human left ventricle actin and myosin complex

EntireName: human left ventricle actin and myosin complex
Components
  • Organelle or cellular component: human left ventricle actin and myosin complex
    • Protein or peptide: Myosin-7
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: human left ventricle actin and myosin complex

SupramoleculeName: human left ventricle actin and myosin complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Myosin-7

MacromoleculeName: Myosin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.41218 KDa
SequenceString: MAVFGAAAPY LRKSEKERLE AQTRPFDLKK DVFVPDDKQE FVKAKIVSRE GGKVTAETEY GKTVTVKEDQ VMQQNPPKFD KIEDMAMLT FLHEPAVLYN LKDRYGSWMI YTYSGLFCVT VNPYKWLPVY TPEVVAAYRG KKRSEAPPHI FSISDNAYQY M LTDRENQS ...String:
MAVFGAAAPY LRKSEKERLE AQTRPFDLKK DVFVPDDKQE FVKAKIVSRE GGKVTAETEY GKTVTVKEDQ VMQQNPPKFD KIEDMAMLT FLHEPAVLYN LKDRYGSWMI YTYSGLFCVT VNPYKWLPVY TPEVVAAYRG KKRSEAPPHI FSISDNAYQY M LTDRENQS ILITGESGAG KTVNTKRVIQ YFAVIAAIGD RSKKDQSPGK GTLEDQIIQA NPALEAFGNA KTVRNDNSSR FG KFIRIHF GATGKLASAD IETYLLEKSR VIFQLKAERD YHIFYQILSN KKPELLDMLL ITNNPYDYAF ISQGETTVAS IDD AEELMA TDNAFDVLGF TSEEKNSMYK LTGAIMHFGN MKFKLKQREE QAEPDGTEEA DKSAYLMGLN SADLLKGLCH PRVK VGNEY VTKGQNVQQV IYATGALAKA VYERMFNWMV TRINATLETK QPRQYFIGVL DIAGFEIFDF NSFEQLCINF TNEKL QQFF NHHMFVLEQE EYKKEGIEWT FIDFGMDLQA CIDLIEKPMG IMSILEEECM FPKATDMTFK AKLFDNHLGK SANFQK PRN IKGKPEAHFS LIHYAGIVDY NIIGWLQKNK DPLNETVVGL YQKSSLKLLS TLFANYAGAD APIEKGKGKA KKGSSFQ TV SALHRENLNK LMTNLRSTHP HFVRCIIPNE TKSPGVMDNP LVMHQLRCNG VLEGIRICRK GFPNRILYGD FRQRYRIL N PAAIPEGQFI DSRKGAEKLL SSLDIDHNQY KFGHTKVFFK AGLLGLLEEM RDERL

UniProtKB: Myosin-7

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Macromolecule #2: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.342145 KDa
SequenceString: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIEHG IITNWDDMEK IWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV P IYEGYALP ...String:
TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIEHG IITNWDDMEK IWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVTHNV P IYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSYEL PD GQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVLSG GTTMYPGIAD RMQKEITALA PST MKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ EYDEAGPSIV HRKCF

UniProtKB: Actin, alpha cardiac muscle 1

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69013
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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