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Yorodumi- PDB-8q4g: Thin filament from FIB milled relaxed left ventricular mouse myof... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q4g | ||||||||||||
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Title | Thin filament from FIB milled relaxed left ventricular mouse myofibrils | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / muscle sarcomere calcium-free cardiac thin-filament | ||||||||||||
Function / homology | Function and homology information actin-mediated cell contraction / RHOB GTPase cycle / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Striated Muscle Contraction / RHOA GTPase cycle / Smooth Muscle Contraction / actin-myosin filament sliding / actin filament-based movement / cardiac myofibril assembly ...actin-mediated cell contraction / RHOB GTPase cycle / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Striated Muscle Contraction / RHOA GTPase cycle / Smooth Muscle Contraction / actin-myosin filament sliding / actin filament-based movement / cardiac myofibril assembly / muscle filament sliding / actin filament capping / cardiac muscle tissue morphogenesis / actomyosin structure organization / ruffle organization / I band / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myosin binding / myofibril / heart contraction / mesenchyme migration / skeletal muscle thin filament assembly / cardiac muscle contraction / positive regulation of stress fiber assembly / sarcomere / positive regulation of cell adhesion / negative regulation of cell migration / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / wound healing / structural constituent of cytoskeleton / disordered domain specific binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / response to ethanol / in utero embryonic development / hydrolase activity / response to xenobiotic stimulus / protein heterodimerization activity / glutamatergic synapse / synapse / positive regulation of gene expression / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8 Å | ||||||||||||
Authors | Tamborrini, D. / Wang, Z. / Wagner, T. / Tacke, S. / Stabrin, M. / Grange, M. / Kho, A.L. / Bennet, P. / Rees, M. / Gautel, M. / Raunser, S. | ||||||||||||
Funding support | European Union, Canada, 3items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q4g.cif.gz | 493.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q4g.ent.gz | 395.1 KB | Display | PDB format |
PDBx/mmJSON format | 8q4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q4g_validation.pdf.gz | 772.6 KB | Display | wwPDB validaton report |
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Full document | 8q4g_full_validation.pdf.gz | 828.5 KB | Display | |
Data in XML | 8q4g_validation.xml.gz | 80.7 KB | Display | |
Data in CIF | 8q4g_validation.cif.gz | 120.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/8q4g ftp://data.pdbj.org/pub/pdb/validation_reports/q4/8q4g | HTTPS FTP |
-Related structure data
Related structure data | 18147MC 8q6tC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: TISSUE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Calcium-free thin filament from relaxed mouse left-ventricular myofibrils Type: TISSUE / Entity ID: #2, #1 / Source: NATURAL |
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Source (natural) | Organism: Mus musculus (house mouse) / Organ: Heart / Tissue: left-ventricular muscle |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 6000 nm / Nominal defocus min: 3000 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 3.4 e/Å2 / Avg electron dose per subtomogram: 140 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100447 / Symmetry type: POINT | |||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 89 / Num. of volumes extracted: 365971 | |||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |