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- PDB-8zb7: Human left ventricle ATM complex -

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Basic information

Entry
Database: PDB / ID: 8zb7
TitleHuman left ventricle ATM complex
Components
  • Actin, alpha cardiac muscle 1
  • Myosin-7
  • Tropomyosin alpha-1 chain
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 / actin filament-based movement / bleb / actin-myosin filament sliding / muscle myosin complex / cardiac myofibril assembly / regulation of muscle contraction ...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 / actin filament-based movement / bleb / actin-myosin filament sliding / muscle myosin complex / cardiac myofibril assembly / regulation of muscle contraction / regulation of the force of heart contraction / Formation of the dystrophin-glycoprotein complex (DGC) / transition between fast and slow fiber / myosin filament / ruffle organization / 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 / structural constituent of muscle / sarcomere organization / RHOB GTPase cycle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / heart contraction / regulation of heart contraction / myosin binding / 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 / RHOA GTPase cycle / Smooth Muscle Contraction / skeletal muscle contraction / striated muscle contraction / ATP metabolic process / cytoskeletal protein binding / cardiac muscle contraction / stress fiber / positive regulation of stress fiber assembly / cytoskeleton organization / positive regulation of cell adhesion / muscle contraction / regulation of heart rate / actin filament organization / negative regulation of cell migration / sarcomere / cellular response to reactive oxygen species / filopodium / actin filament / wound healing / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / Z disc / actin filament binding / regulation of cell shape / actin cytoskeleton / lamellipodium / actin binding / cell body / response to ethanol / blood microparticle / cytoskeleton / calmodulin binding / hydrolase activity / response to xenobiotic stimulus / 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
ADENOSINE-5'-DIPHOSPHATE / Tropomyosin alpha-1 chain / Myosin-7 / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLi, D.N. / Zhao, Q.Y. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human left ventricle ATM complex
Authors: Li, D.N. / Zhao, Q.Y. / Liu, C.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Myosin-7
B: Actin, alpha cardiac muscle 1
C: Actin, alpha cardiac muscle 1
D: Actin, alpha cardiac muscle 1
E: Actin, alpha cardiac muscle 1
F: Actin, alpha cardiac muscle 1
O: Tropomyosin alpha-1 chain
P: Tropomyosin alpha-1 chain
G: Myosin-7
H: Myosin-7
I: Myosin-7
J: Myosin-7
K: Myosin-7
A: Actin, alpha cardiac muscle 1
L: Tropomyosin alpha-1 chain
N: Tropomyosin alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)857,09022
Polymers854,52716
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Myosin-7 / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac ...Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 88412.180 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P12883
#2: Protein
Actin, alpha cardiac muscle 1 / Alpha-cardiac actin


Mass: 41342.145 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P68032, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 19000.168 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09493
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Human left ventricle ATM complex / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -166.66 ° / Axial rise/subunit: 27.3 Å / Axial symmetry: C1
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69013 / Symmetry type: HELICAL

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