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Yorodumi- PDB-7nep: Homology model of the in situ actomyosin complex from the A-band ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nep | ||||||||||||||||||
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Title | Homology model of the in situ actomyosin complex from the A-band of mouse psoas muscle sarcomere in the rigor state | ||||||||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Muscle proteins / force generation / sarcomere / cytoskeleton | ||||||||||||||||||
Function / homology | Function and homology information positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / : / skeletal muscle fiber adaptation / Striated Muscle Contraction / Smooth Muscle Contraction / contractile muscle fiber / muscle filament sliding / : / myosin filament ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / : / skeletal muscle fiber adaptation / Striated Muscle Contraction / Smooth Muscle Contraction / contractile muscle fiber / muscle filament sliding / : / myosin filament / actin filament capping / ruffle organization / myosin II complex / myosin complex / response to steroid hormone / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myofibril / mesenchyme migration / skeletal muscle thin filament assembly / striated muscle thin filament / positive regulation of cell adhesion / skeletal muscle fiber development / muscle contraction / cardiac muscle contraction / stress fiber / response to mechanical stimulus / skeletal muscle tissue development / positive regulation of stress fiber assembly / negative regulation of cell migration / filopodium / response to activity / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / wound healing / structural constituent of cytoskeleton / actin filament binding / disordered domain specific binding / double-stranded RNA binding / actin cytoskeleton / lamellipodium / actin binding / cell body / in utero embryonic development / calmodulin binding / hydrolase activity / immune response / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / 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: 10.2 Å | ||||||||||||||||||
Authors | Wang, Z. / Grange, M. / Wagner, T. / Kho, A.L. / Gautel, M. / Raunser, S. | ||||||||||||||||||
Funding support | Germany, United Kingdom, European Union, 5items
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Citation | Journal: Cell / Year: 2021 Title: The molecular basis for sarcomere organization in vertebrate skeletal muscle. Authors: Zhexin Wang / Michael Grange / Thorsten Wagner / Ay Lin Kho / Mathias Gautel / Stefan Raunser / Abstract: Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we ...Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we determine the molecular architecture of native vertebrate skeletal sarcomeres by electron cryo-tomography. Our reconstruction reveals molecular details of the three-dimensional organization and interaction of actin and myosin in the A-band, I-band, and Z-disc and demonstrates that α-actinin cross-links antiparallel actin filaments by forming doublets with 6-nm spacing. Structures of myosin, tropomyosin, and actin at ~10 Å further reveal two conformations of the "double-head" myosin, where the flexible orientation of the lever arm and light chains enable myosin not only to interact with the same actin filament, but also to split between two actin filaments. Our results provide unexpected insights into the fundamental organization of vertebrate skeletal muscle and serve as a strong foundation for future investigations of muscle diseases. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nep.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7nep.ent.gz | 999.4 KB | Display | PDB format |
PDBx/mmJSON format | 7nep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nep_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7nep_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7nep_validation.xml.gz | 184.8 KB | Display | |
Data in CIF | 7nep_validation.cif.gz | 284.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/7nep ftp://data.pdbj.org/pub/pdb/validation_reports/ne/7nep | HTTPS FTP |
-Related structure data
Related structure data | 12289MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 41747.527 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68134 #2: Protein | Mass: 28922.074 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P58771 #3: Protein | Mass: 92518.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5SX39 #4: Protein | Mass: 16573.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05977 #5: Protein | Mass: 16326.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97457 |
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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
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Molecular weight |
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Source (natural) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was myofibrils. | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Calibrated magnification: 28409 X / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 3.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 8 / Used frames/image: 1-8 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18090 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 8 / Num. of volumes extracted: 32421 | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||
Atomic model building |
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