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- EMDB-39904: Mouse left ventricle ATM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39904
TitleMouse left ventricle ATM complex
Map data
Sample
  • Complex: Mouse left ventricle ATM complex
    • Protein or peptide: Myosin-6
    • Protein or peptide: Actin, alpha cardiac muscle 1
    • Protein or peptide: Tropomyosin alpha-1 chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsprotein fibril / complex
Function / homology
Function and homology information


visceral muscle development / regulation of heart growth / atrial cardiac muscle tissue morphogenesis / myofibril assembly / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / cytoplasmic actin-based contraction involved in cell motility ...visceral muscle development / regulation of heart growth / atrial cardiac muscle tissue morphogenesis / myofibril assembly / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / cytoplasmic actin-based contraction involved in cell motility / RHOA GTPase cycle / Smooth Muscle Contraction / 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 / cardiac muscle contraction / stress fiber / regulation of heart rate / filopodium / actin filament / structural constituent of cytoskeleton / 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 / actin cytoskeleton / cell body / response to ethanol / in utero embryonic development / calmodulin binding / hydrolase activity / response to xenobiotic stimulus / protein heterodimerization activity / synapse / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / glutamatergic synapse / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / 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. ...Tropomyosins signature. / Tropomyosin / Tropomyosin / 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
Tropomyosin alpha-1 chain / Actin, alpha cardiac muscle 1 / Myosin-6
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsLi DN / Zhao QY / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be published
Title: Cryo-EM structure of Mouse left ventricle ATM complex
Authors: Li DN / Zhao QY / Liu C
History
DepositionApr 26, 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_39904.png

Downloads & links

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Map

FileDownload / File: emd_39904.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: 0.005
Minimum - Maximum-0.0050267386 - 0.02024331
Average (Standard dev.)0.00021227088 (±0.001113625)
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_39904_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_39904_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 left ventricle ATM complex

EntireName: Mouse left ventricle ATM complex
Components
  • Complex: Mouse left ventricle ATM complex
    • Protein or peptide: Myosin-6
    • Protein or peptide: Actin, alpha cardiac muscle 1
    • Protein or peptide: Tropomyosin alpha-1 chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Mouse left ventricle ATM complex

SupramoleculeName: Mouse left ventricle ATM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Myosin-6

MacromoleculeName: Myosin-6 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 87.722945 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 RVKVG 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 #2: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / 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)
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 #3: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.727119 KDa
SequenceString:
QLVEEELDRA QERLATALQK LEEAEKAADE SERGMKVIES RAQKDEEKME IQEIQLKEAK HIAEDADRKY EEVARKLVII ESDLERAEE RAELSEGKCA ELEEELKTVT NNLKSLEAQA EKYSQKEDKY EEEIKVLSDK LKEAETRAEF AERSVTKLEK S IDDLEDEL YAQKLKYKAI

UniProtKB: Tropomyosin alpha-1 chain

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / 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
Processinghelical 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

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.71 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.80 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5443
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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