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Yorodumi- PDB-8q6t: Helical reconstruction of the relaxed thick filament from FIB mil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q6t | ||||||||||||||||||
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Title | Helical reconstruction of the relaxed thick filament from FIB milled left ventricular mouse myofibrils | ||||||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Mammalian / Muscle / Thick filament / Cardiac | ||||||||||||||||||
Function / homology | Function and homology information forward locomotion / heart growth / striated muscle cell development / regulation of relaxation of cardiac muscle / muscle cell fate specification / Striated Muscle Contraction / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / contractile muscle fiber / cardiac myofibril ...forward locomotion / heart growth / striated muscle cell development / regulation of relaxation of cardiac muscle / muscle cell fate specification / Striated Muscle Contraction / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / contractile muscle fiber / cardiac myofibril / regulation of striated muscle contraction / cardiac myofibril assembly / transition between fast and slow fiber / muscle myosin complex / muscle filament sliding / ventricular system development / regulation of the force of heart contraction / detection of muscle stretch / myosin filament / muscle cell development / cardiac muscle tissue morphogenesis / cardiac muscle hypertrophy in response to stress / adult heart development / myosin II complex / M band / I band / cardiac muscle tissue development / myosin complex / A band / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / ankyrin binding / intracellular non-membrane-bounded organelle / sarcomere organization / microfilament motor activity / myofibril / heart contraction / positive regulation of the force of heart contraction / cytoskeletal motor activity / skeletal muscle contraction / actin monomer binding / somitogenesis / heart morphogenesis / striated muscle contraction / stress fiber / cardiac muscle contraction / muscle contraction / ATP metabolic process / sarcomere / regulation of heart rate / post-embryonic development / negative regulation of cell growth / structural constituent of cytoskeleton / Z disc / actin filament binding / actin cytoskeleton / heart development / protein tyrosine kinase activity / in utero embryonic development / cytoskeleton / non-specific serine/threonine protein kinase / calmodulin binding / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / protein-containing complex binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 18 Å | ||||||||||||||||||
Authors | Tamborrini, D. / Raunser, S. | ||||||||||||||||||
Funding support | Germany, European Union, United Kingdom, 5items
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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 | 8q6t.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8q6t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8q6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q6t_validation.pdf.gz | 794.1 KB | Display | wwPDB validaton report |
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Full document | 8q6t_full_validation.pdf.gz | 896.7 KB | Display | |
Data in XML | 8q6t_validation.xml.gz | 337.4 KB | Display | |
Data in CIF | 8q6t_validation.cif.gz | 555.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/8q6t ftp://data.pdbj.org/pub/pdb/validation_reports/q6/8q6t | HTTPS FTP |
-Related structure data
Related structure data | 18198MC 8q4gC 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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1 |
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-Components
#1: Protein | Mass: 223226.531 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91Z83 #2: Protein | Mass: 17243.553 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P09542 #3: Protein | Mass: 18259.512 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51667 #4: Protein | Mass: 44777.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3TF37 #5: Protein | Mass: 118766.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2ASS6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Relaxed thick filament; A-band region; C-type super-repeat Type: CELL Details: Single asymmetrical unit from the relaxed thick filament obtained from FIB milled left ventricular mouse myofibrils Entity ID: #1-#3, #5, #4 / Source: NATURAL |
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Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 7.1 |
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 | |||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 0 ° / Axial rise/subunit: 430 Å / Axial symmetry: C3 | |||||||||||||||||||||
3D reconstruction | Resolution: 18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1589 Details: Helical reconstruction containing 4.5x repeats extrapolated from a 3x repeat reconstruction (EMD-18146) Symmetry type: HELICAL | |||||||||||||||||||||
EM volume selection | Num. of tomograms: 89 / Num. of volumes extracted: 67492 | |||||||||||||||||||||
Atomic model building |
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