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- EMDB-39896: Human left ventricle ATM complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39896
TitleHuman left ventricle ATM complex
Map dataEM map
Sample
  • Complex: Human left ventricle ATM complex
    • Protein or peptide: Myosin-7
    • Protein or peptide: Actin, alpha cardiac muscle 1
    • Protein or peptide: Tropomyosin alpha-1 chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsprotein fibril / protein complex
Function / homology
Function and homology information


regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / bleb / actin filament-based movement / muscle myosin complex / actin-myosin filament sliding / regulation of muscle contraction / cardiac myofibril assembly ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / bleb / actin filament-based movement / muscle myosin complex / actin-myosin filament sliding / regulation of muscle contraction / cardiac myofibril assembly / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / ruffle organization / adult heart development / cardiac muscle tissue morphogenesis / positive regulation of ATP-dependent activity / actomyosin structure organization / cardiac muscle hypertrophy in response to stress / Striated Muscle Contraction / muscle filament sliding / myosin complex / myosin II complex / I band / structural constituent of muscle / sarcomere organization / RHOB GTPase cycle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / heart contraction / myosin binding / regulation of heart contraction / negative regulation of vascular associated smooth muscle cell migration / myofibril / mesenchyme migration / negative regulation of vascular associated smooth muscle cell proliferation / skeletal muscle thin filament assembly / Smooth Muscle Contraction / RHOA GTPase cycle / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / stress fiber / cytoskeletal protein binding / cardiac muscle contraction / positive regulation of stress fiber assembly / muscle contraction / cytoskeleton organization / positive regulation of cell adhesion / regulation of heart rate / negative regulation of cell migration / sarcomere / actin filament organization / filopodium / cellular response to reactive oxygen species / actin filament / wound healing / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / Z disc / ruffle membrane / actin filament binding / lamellipodium / actin cytoskeleton / regulation of cell shape / actin binding / cell body / blood microparticle / cytoskeleton / hydrolase activity / calmodulin binding / protein heterodimerization activity / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / protein homodimerization activity / extracellular space / extracellular exosome / ATP binding / identical protein binding / membrane / cytosol / 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. / 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. / 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 / Myosin-7 / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLi DN / Zhao QY / Liu C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human 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_39896.png

Downloads & links

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Map

FileDownload / File: emd_39896.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
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: 0.006
Minimum - Maximum-0.018936908 - 0.057186075
Average (Standard dev.)0.0003527056 (±0.0019284289)
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_39896_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_39896_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 ATM complex

EntireName: Human left ventricle ATM complex
Components
  • Complex: Human left ventricle ATM complex
    • Protein or peptide: Myosin-7
    • 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: Human left ventricle ATM complex

SupramoleculeName: Human left ventricle ATM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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: 6 / 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: 6 / 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: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.000168 KDa
SequenceString:
SLQKKLKGTE DELDKYSEAL KDAQEKLELA EKKATDAEAD VASLNRRIQL VEEELDRAQE RLATALQKLE EAEKAADESE RGMKVIESR AQKDEEKMEI QEIQLKEAKH IAEDADRKYE EVARKLVIIE SDLERAEERA ELSEGKCAEL EEELKTVTNN L KSLEAQ

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: 27.3 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.66 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69013
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8efi

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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