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- PDB-8zbk: Mouse left ventricle ATM complex -

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Basic information

Entry
Database: PDB / ID: 8zbk
TitleMouse left ventricle ATM complex
Components
  • Actin, alpha cardiac muscle 1
  • Myosin-6
  • Tropomyosin alpha-1 chain
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 / regulation of heart contraction / myosin binding / 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 / regulation of blood pressure / 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 / 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
ADENOSINE-5'-DIPHOSPHATE / Tropomyosin alpha-1 chain / Actin, alpha cardiac muscle 1 / Myosin-6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsLi, D.N. / Zhao, Q.Y. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be published
Title: Cryo-EM structure of Mouse 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

Downloads & links

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Assembly

Deposited unit
A: Myosin-6
B: Actin, alpha cardiac muscle 1
I: Actin, alpha cardiac muscle 1
J: Actin, alpha cardiac muscle 1
D: Actin, alpha cardiac muscle 1
K: Actin, alpha cardiac muscle 1
M: Actin, alpha cardiac muscle 1
R: Tropomyosin alpha-1 chain
T: Tropomyosin alpha-1 chain
S: Tropomyosin alpha-1 chain
U: Tropomyosin alpha-1 chain
C: Myosin-6
F: Myosin-6
G: Myosin-6
H: Myosin-6
L: Myosin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)858,97922
Polymers856,41616
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Myosin-6 / Myosin heavy chain 6 / Myosin heavy chain / cardiac muscle alpha isoform / MyHC-alpha


Mass: 87722.945 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q02566
#2: Protein
Actin, alpha cardiac muscle 1 / Alpha-cardiac actin


Mass: 41194.973 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68033, 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: 20727.119 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P58771
#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 modificationY

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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: Mouse left ventricle ATM complex / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
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

EM softwareName: PHENIX / Version: 1.15.2_3472: / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -166.8 ° / Axial rise/subunit: 27.71 Å / Axial symmetry: C1
3D reconstructionResolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5443 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00658894
ELECTRON MICROSCOPYf_angle_d0.68179422
ELECTRON MICROSCOPYf_dihedral_angle_d14.8235802
ELECTRON MICROSCOPYf_chiral_restr0.0448676
ELECTRON MICROSCOPYf_plane_restr0.00410254

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