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- EMDB-60130: Mouse MYH6 R404Q left ventricle actin and myosin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60130
TitleMouse MYH6 R404Q left ventricle actin and myosin complex
Map data
Sample
  • Organelle or cellular component: Mouse MYH6 R404Q left ventricle actin and myosin complex
    • Protein or peptide: Actin, alpha cardiac muscle 1
    • Protein or peptide: Myosin-6
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsprotein binding / actin / myosin
Function / homology
Function and homology information


visceral muscle development / regulation of heart growth / atrial cardiac muscle tissue morphogenesis / myofibril assembly / actin-mediated cell contraction / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / RHOA GTPase cycle / actin filament-based movement ...visceral muscle development / regulation of heart growth / atrial cardiac muscle tissue morphogenesis / myofibril assembly / actin-mediated cell contraction / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / RHOA GTPase cycle / actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle tissue morphogenesis / actomyosin structure organization / cardiac muscle hypertrophy in response to stress / muscle filament sliding / myosin complex / I band / cardiac muscle cell development / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myosin binding / regulation of heart contraction / myofibril / mesenchyme migration / skeletal muscle thin filament assembly / striated muscle contraction / ATP metabolic process / stress fiber / cardiac muscle contraction / regulation of heart rate / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of blood pressure / Z disc / actin filament binding / lamellipodium / cell body / in utero embryonic development / response to ethanol / hydrolase activity / calmodulin binding / response to xenobiotic stimulus / synapse / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / ATP binding
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. / Myosin head, motor domain / Myosin head (motor domain) / 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / 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
Actin, alpha cardiac muscle 1 / Myosin-6
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsLi DN / Zhao QY / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mouse MYH6 R404Q left ventricle actin and myosin complex
Authors: Li DN / Zhao QY / Liu C
History
DepositionMay 14, 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_60130.png

Downloads & links

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Map

FileDownload / File: emd_60130.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: 0.015
Minimum - Maximum-0.028103327 - 0.067582965
Average (Standard dev.)0.000036317935 (±0.00080969103)
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: #2

Fileemd_60130_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60130_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 : Mouse MYH6 R404Q left ventricle actin and myosin complex

EntireName: Mouse MYH6 R404Q left ventricle actin and myosin complex
Components
  • Organelle or cellular component: Mouse MYH6 R404Q left ventricle actin and myosin complex
    • Protein or peptide: Actin, alpha cardiac muscle 1
    • Protein or peptide: Myosin-6
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Mouse MYH6 R404Q left ventricle actin and myosin complex

SupramoleculeName: Mouse MYH6 R404Q left ventricle actin and myosin complex
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / type: protein_or_peptide / ID: 1 / 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: Mus musculus (house mouse) / Strain: C57BL/6JGpt
Molecular weightTheoretical: 41.194973 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 HRKC

UniProtKB: Actin, alpha cardiac muscle 1

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Macromolecule #2: Myosin-6

MacromoleculeName: Myosin-6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Strain: C57BL/6JGpt
Molecular weightTheoretical: 87.693883 KDa
SequenceString: AQMADFGAAA QYLRKSEKER LEAQTRPFDI RTECFVPDDK EEYVKAKVVS REGGKVTAET ENGKTVTIKE DQVMQQNPPK FDKIEDMAM LTFLHEPAVL YNLKERYAAW MIYTYSGLFC VTVNPYKWLP VYNAEVVAAY RGKKRSEAPP HIFSISDNAY Q YMLTDREN ...String:
AQMADFGAAA QYLRKSEKER LEAQTRPFDI RTECFVPDDK EEYVKAKVVS REGGKVTAET ENGKTVTIKE DQVMQQNPPK FDKIEDMAM LTFLHEPAVL YNLKERYAAW MIYTYSGLFC VTVNPYKWLP VYNAEVVAAY RGKKRSEAPP HIFSISDNAY Q YMLTDREN QSILITGESG AGKTVNTKRV IQYFASIAAI GDRSKKENPN ANKGTLEDQI IQANPALEAF GNAKTVRNDN SS RFGKFIR IHFGATGKLA SADIETYLLE KSRVIFQLKA ERNYHIFYQI LSNKKPELLD MLLVTNNPYD YAFVSQGEVS VAS IDDSEE LLATDSAFDV LSFTAEEKAG VYKLTGAIMH YGNMKFKQKQ REEQAEPDGT EDADKSAYLM GLNSADLLKG LCHP QVKVG NEYVTKGQSV QQVYYSIGAL AKSVYEKMFN WMVTRINATL ETKQPRQYFI GVLDIAGFEI FDFNSFEQLC INFTN EKLQ QFFNHHMFVL EQEEYKKEGI EWEFIDFGMD LQACIDLIEK PMGIMSILEE ECMFPKASDM TFKAKLYDNH LGKSNN FQK PRNVKGKQEA HFSLVHYAGT VDYNIMGWLE KNKDPLNETV VGLYQKSSLK LMATLFSTYA SADTGDSGKG KGGKKKG SS FQTVSALHRE NLNKLMTNLK TTHPHFVRCI IPNERKAPGV MDNPLVMHQL RCNGVLEGIR ICRKGFPNRI LYGDFRQR Y RILNPAAIPE GQFIDSRKGA EKLLGSLDID HNQYKFGHTK VFFKAGLLGL L

UniProtKB: Myosin-6

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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: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92110
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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