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- PDB-8q4g: Thin filament from FIB milled relaxed left ventricular mouse myof... -

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Basic information

Entry
Database: PDB / ID: 8q4g
TitleThin filament from FIB milled relaxed left ventricular mouse myofibrils
Components
  • Actin, alpha cardiac muscle 1
  • Tropomyosin alpha-1 chain
KeywordsSTRUCTURAL PROTEIN / muscle sarcomere calcium-free cardiac thin-filament
Function / homology
Function and homology information


regulation of ATP-dependent activity / 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 / Regulation of CDH1 Function / RHOA GTPase cycle / Smooth Muscle Contraction ...regulation of ATP-dependent activity / 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 / Regulation of CDH1 Function / RHOA GTPase cycle / Smooth Muscle Contraction / actin-myosin filament sliding / cardiac myofibril assembly / actin filament-based movement / cardiac muscle tissue morphogenesis / bleb / ruffle organization / positive regulation of ATP-dependent activity / actomyosin structure organization / actin filament capping / muscle filament sliding / sarcomere organization / I band / heart contraction / ventricular cardiac muscle tissue morphogenesis / myosin binding / microfilament motor activity / negative regulation of vascular associated smooth muscle cell migration / mesenchyme migration / myofibril / negative regulation of vascular associated smooth muscle cell proliferation / skeletal muscle thin filament assembly / cardiac muscle contraction / positive regulation of stress fiber assembly / cytoskeletal protein binding / stress fiber / positive regulation of cell adhesion / negative regulation of cell migration / actin filament organization / wound healing / sarcomere / actin filament / filopodium / in utero embryonic development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / structural constituent of cytoskeleton / disordered domain specific binding / regulation of cell shape / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / response to ethanol / response to xenobiotic stimulus / protein heterodimerization activity / hydrolase activity / positive regulation of gene expression / synapse / negative regulation of apoptotic process / glutamatergic synapse / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...Tropomyosins signature. / Tropomyosin / Tropomyosin / 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
Similarity search - Domain/homology
Tropomyosin alpha-1 chain / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8 Å
AuthorsTamborrini, D. / Wang, Z. / Wagner, T. / Tacke, S. / Stabrin, M. / Grange, M. / Kho, A.L. / Bennet, P. / Rees, M. / Gautel, M. / Raunser, S.
Funding supportEuropean Union, Canada, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)European Union
Medical Research Council (MRC, Canada)MR/R003106/1 Canada
European Research Council (ERC)European Union
CitationJournal: Nature / Year: 2023
Title: Structure of the native myosin filament in the relaxed cardiac sarcomere.
Authors: Davide Tamborrini / Zhexin Wang / Thorsten Wagner / Sebastian Tacke / Markus Stabrin / Michael Grange / Ay Lin Kho / Martin Rees / Pauline Bennett / Mathias Gautel / Stefan Raunser /
Abstract: The thick filament is a key component of sarcomeres, the basic units of striated muscle. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other ...The thick filament is a key component of sarcomeres, the basic units of striated muscle. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other heart and muscle diseases. Despite the central importance of the thick filament, its molecular organization remains unclear. Here we present the molecular architecture of native cardiac sarcomeres in the relaxed state, determined by cryo-electron tomography. Our reconstruction of the thick filament reveals the three-dimensional organization of myosin, titin and myosin-binding protein C (MyBP-C). The arrangement of myosin molecules is dependent on their position along the filament, suggesting specialized capacities in terms of strain susceptibility and force generation. Three pairs of titin-α and titin-β chains run axially along the filament, intertwining with myosin tails and probably orchestrating the length-dependent activation of the sarcomere. Notably, whereas the three titin-α chains run along the entire length of the thick filament, titin-β chains do not. The structure also demonstrates that MyBP-C bridges thin and thick filaments, with its carboxy-terminal region binding to the myosin tails and directly stabilizing the OFF state of the myosin heads in an unforeseen manner. These results provide a foundation for future research investigating muscle disorders involving sarcomeric components.
History
DepositionAug 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
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
G: Tropomyosin alpha-1 chain
H: Tropomyosin alpha-1 chain
I: Actin, alpha cardiac muscle 1


Theoretical massNumber of molelcules
Total (without water)331,9799
Polymers331,9799
Non-polymers00
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
Actin, alpha cardiac muscle 1 / Alpha-cardiac actin


Mass: 41471.258 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: HEART / Tissue: left-ventricular muscle
References: UniProt: P68033, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 20840.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: HEART / Tissue: left-ventricular muscle / References: UniProt: P58771
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Calcium-free thin filament from relaxed mouse left-ventricular myofibrils
Type: TISSUE / Entity ID: #2, #1 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse) / Organ: Heart / Tissue: left-ventricular muscle
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 magnification: 81000 X / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.4 e/Å2 / Avg electron dose per subtomogram: 140 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1Warpvolume selection
2SerialEMimage acquisition
4WarpCTF correction
5RELIONCTF correction
8UCSF ChimeraXmodel fitting
11RELIONfinal Euler assignment
13RELION3D reconstruction
14NAMDmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100447 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 89 / Num. of volumes extracted: 365971
Atomic model buildingSource name: AlphaFold / Type: in silico model

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