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Yorodumi- PDB-8efd: Human cardiac myosin II and associated essential light chain in t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8efd | ||||||
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Title | Human cardiac myosin II and associated essential light chain in the rigor conformation | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / actin / tropomyosin / myosin / cardiac | ||||||
Function / homology | Function and homology information Striated Muscle Contraction / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / contractile muscle fiber / transition between fast and slow fiber / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / myosin filament / cardiac muscle hypertrophy in response to stress ...Striated Muscle Contraction / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / contractile muscle fiber / transition between fast and slow fiber / muscle myosin complex / muscle filament sliding / regulation of the force of heart contraction / myosin filament / cardiac muscle hypertrophy in response to stress / adult heart development / myosin II complex / myosin complex / ventricular cardiac muscle tissue morphogenesis / structural constituent of muscle / sarcomere organization / microfilament motor activity / myofibril / skeletal muscle contraction / striated muscle contraction / stress fiber / cardiac muscle contraction / muscle contraction / ATP metabolic process / sarcomere / regulation of heart rate / Z disc / actin filament binding / calmodulin binding / calcium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Doran, M.H. / Lehman, W. / Rynkiewicz, M.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Gen Physiol / Year: 2023 Title: Conformational changes linked to ADP release from human cardiac myosin bound to actin-tropomyosin. Authors: Matthew H Doran / Michael J Rynkiewicz / David Rasicci / Skylar M L Bodt / Meaghan E Barry / Esther Bullitt / Christopher M Yengo / Jeffrey R Moore / William Lehman / Abstract: Following binding to the thin filament, β-cardiac myosin couples ATP-hydrolysis to conformational rearrangements in the myosin motor that drive myofilament sliding and cardiac ventricular ...Following binding to the thin filament, β-cardiac myosin couples ATP-hydrolysis to conformational rearrangements in the myosin motor that drive myofilament sliding and cardiac ventricular contraction. However, key features of the cardiac-specific actin-myosin interaction remain uncertain, including the structural effect of ADP release from myosin, which is rate-limiting during force generation. In fact, ADP release slows under experimental load or in the intact heart due to the afterload, thereby adjusting cardiac muscle power output to meet physiological demands. To further elucidate the structural basis of this fundamental process, we used a combination of cryo-EM reconstruction methodologies to determine structures of the human cardiac actin-myosin-tropomyosin filament complex at better than 3.4 Å-resolution in the presence and in the absence of Mg2+·ADP. Focused refinements of the myosin motor head and its essential light chains in these reconstructions reveal that small changes in the nucleotide-binding site are coupled to significant rigid body movements of the myosin converter domain and a 16-degree lever arm swing. Our structures provide a mechanistic framework to understand the effect of ADP binding and release on human cardiac β-myosin, and offer insights into the force-sensing mechanism displayed by the cardiac myosin motor. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8efd.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8efd.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 8efd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8efd_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8efd_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8efd_validation.xml.gz | 46 KB | Display | |
Data in CIF | 8efd_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/8efd ftp://data.pdbj.org/pub/pdb/validation_reports/ef/8efd | HTTPS FTP |
-Related structure data
Related structure data | 28080MC 8efeC 8efhC M: map data used to model this data C: citing same article (ref.) |
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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: 99157.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MYH7, MYHCB / Cell line (production host): C2C12 / Production host: Mus musculus (house mouse) / References: UniProt: P12883 |
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#2: Protein | Mass: 20620.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: C2C12 / References: UniProt: P05977 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Mus musculus (house mouse) / Cell: C2C12 | ||||||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||||||
Specimen | Conc.: 0.13 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: This complex was part of a larger filament containing actin-tropomyosin. The map was a result of a focused single particle approach. | ||||||||||||||||||||||||
Specimen support | Details: 15 mA was used in the Pelco Easiglow glow discharge machine Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 80000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.12 sec. / Electron dose: 53.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 3961 |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 35 / Used frames/image: 1-35 |
-Processing
Software | Name: PHENIX / Version: 1.19.1_4122: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 176178 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88048 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6X5Z Accession code: 6X5Z / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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