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- PDB-7jh7: cardiac actomyosin complex -

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Basic information

Entry
Database: PDB / ID: 7jh7
Titlecardiac actomyosin complex
Components
  • Actin, alpha cardiac muscle 1
  • Myosin-7
  • tropomyosin
KeywordsMOTOR PROTEIN / actomyosin
Function / homology
Function and homology information


RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / actin-myosin filament sliding / myosin filament / myosin complex / myosin binding / myofibril / mesenchyme migration / heart contraction ...RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / actin-myosin filament sliding / myosin filament / myosin complex / myosin binding / myofibril / mesenchyme migration / heart contraction / cytoskeletal motor activity / sarcomere / filopodium / actin filament organization / actin filament / actin filament binding / lamellipodium / cell body / calmodulin binding / positive regulation of gene expression / ATP binding / cytoplasm
Similarity search - Function
: / 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 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. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / 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 / Actin, alpha cardiac muscle 1 / Myosin-7
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGalkin, V.E. / Schroeder, G.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL140925 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116790 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116788 United States
CitationJournal: Structure / Year: 2021
Title: High-Resolution Cryo-EM Structure of the Cardiac Actomyosin Complex.
Authors: Cristina Risi / Luisa U Schäfer / Betty Belknap / Ian Pepper / Howard D White / Gunnar F Schröder / Vitold E Galkin /
Abstract: Heart contraction depends on a complicated array of interactions between sarcomeric proteins required to convert chemical energy into mechanical force. Cyclic interactions between actin and myosin ...Heart contraction depends on a complicated array of interactions between sarcomeric proteins required to convert chemical energy into mechanical force. Cyclic interactions between actin and myosin molecules, controlled by troponin and tropomyosin, generate the sliding force between the actin-based thin and myosin-based thick filaments. Alterations in this sophisticated system due to missense mutations can lead to cardiovascular diseases. Numerous structural studies proposed pathological mechanisms of missense mutations at the myosin-myosin, actin-tropomyosin, and tropomyosin-troponin interfaces. However, despite the central role of actomyosin interactions a detailed structural description of the cardiac actomyosin interface remained unknown. Here, we report a cryo-EM structure of a cardiac actomyosin complex at 3.8 Å resolution. The structure reveals the molecular basis of cardiac diseases caused by missense mutations in myosin and actin proteins.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
F: Myosin-7
B: Actin, alpha cardiac muscle 1
G: Myosin-7
C: Actin, alpha cardiac muscle 1
H: Myosin-7
E: Actin, alpha cardiac muscle 1
D: Actin, alpha cardiac muscle 1
I: tropomyosin
J: tropomyosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)906,54420
Polymers904,28610
Non-polymers2,25810
Water0
1


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

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Components

#1: Protein
Actin, alpha cardiac muscle 1 / / Cardiac muscle alpha actin 1


Mass: 42064.891 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: ventricle / References: UniProt: B6VNT8
#2: 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: 223649.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: ventricle / References: UniProt: P79293
#3: Protein tropomyosin /


Mass: 11507.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: ventricle
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: porcine native cardiac thin filament decorated with porcine cardiac myosin-S1
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 492 kDa/nm / Experimental value: NO
Source (natural)Organism: Sus scrofa (pig) / Organ: heart / Tissue: ventricular
Buffer solutionpH: 7
SpecimenConc.: 0.09 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 3 uL of 2 uM TFs were applied to glow-discharged lacey carbon grid for 1 min, gently blotted with Whatman #1 filter paper, and incubated with 2 uL of myosin-S1 [1.2 uM] for 2 min
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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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 FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2373

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
1EMANparticle selection
4CTFFIND4CTF correction
7DireXmodel fitting
9PHENIX1.17model refinement
10RELION3.08initial Euler assignment
11RELION3.08final Euler assignment
12RELION3.08classification
13RELION3.083D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.7 ° / Axial rise/subunit: 27.3 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115746 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: SWISS-MODEL web service used to create initial homology models of cardiac actin and myosin
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00634474
ELECTRON MICROSCOPYf_angle_d0.97146633
ELECTRON MICROSCOPYf_dihedral_angle_d8.16324347
ELECTRON MICROSCOPYf_chiral_restr0.0585177
ELECTRON MICROSCOPYf_plane_restr0.0086055

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