+Open data
-Basic information
Entry | Database: PDB / ID: 7qin | ||||||||||||||||||
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Title | In situ structure of actomyosin complex in skeletal sarcomere | ||||||||||||||||||
Components |
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Keywords | CONTRACTILE PROTEIN / Skeletal muscle / Sarcomere / Thin filament / Cross-bridge | ||||||||||||||||||
Function / homology | Function and homology information skeletal muscle fiber adaptation / Striated Muscle Contraction / : / myosin filament / : / response to steroid hormone / myosin II complex / microfilament motor activity / myofibril / mesenchyme migration ...skeletal muscle fiber adaptation / Striated Muscle Contraction / : / myosin filament / : / response to steroid hormone / myosin II complex / microfilament motor activity / myofibril / mesenchyme migration / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / response to mechanical stimulus / stress fiber / response to activity / filopodium / muscle contraction / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-stranded RNA binding / actin filament binding / lamellipodium / cell body / hydrolase activity / calmodulin binding / positive regulation of gene expression / protein-containing complex / ATP binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.6 Å | ||||||||||||||||||
Authors | Wang, Z. / Grange, M. / Pospich, S. / Wagner, T. / Kho, A.L. / Gautel, M. / Raunser, S. | ||||||||||||||||||
Funding support | European Union, 5items
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Citation | Journal: Science / Year: 2022 Title: Structures from intact myofibrils reveal mechanism of thin filament regulation through nebulin. Authors: Zhexin Wang / Michael Grange / Sabrina Pospich / Thorsten Wagner / Ay Lin Kho / Mathias Gautel / Stefan Raunser / Abstract: In skeletal muscle, nebulin stabilizes and regulates the length of thin filaments, but the underlying mechanism remains nebulous. In this work, we used cryo-electron tomography and subtomogram ...In skeletal muscle, nebulin stabilizes and regulates the length of thin filaments, but the underlying mechanism remains nebulous. In this work, we used cryo-electron tomography and subtomogram averaging to reveal structures of native nebulin bound to thin filaments within intact sarcomeres. This in situ reconstruction provided high-resolution details of the interaction between nebulin and actin, demonstrating the stabilizing role of nebulin. Myosin bound to the thin filaments exhibited different conformations of the neck domain, highlighting its inherent structural variability in muscle. Unexpectedly, nebulin did not interact with myosin or tropomyosin, but it did interact with a troponin T linker through two potential binding motifs on nebulin, explaining its regulatory role. Our structures support the role of nebulin as a thin filament "molecular ruler" and provide a molecular basis for studying nemaline myopathies. | ||||||||||||||||||
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 | 7qin.cif.gz | 634.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qin.ent.gz | 541 KB | Display | PDB format |
PDBx/mmJSON format | 7qin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qin_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7qin_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7qin_validation.xml.gz | 112.4 KB | Display | |
Data in CIF | 7qin_validation.cif.gz | 158.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qin ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qin | HTTPS FTP |
-Related structure data
Related structure data | 13991MC 7qimC 7qioC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 9 molecules ABCDEFGLM
#1: Protein | Mass: 41387.227 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68134 #2: Protein | | Mass: 9188.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Model with conserved tyrosines of three nebulin simple repeats Source: (natural) Mus musculus (house mouse) #3: Protein | | Mass: 6131.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Model with conserved tyrosines of two nebulin simple repeats Source: (natural) Mus musculus (house mouse) #7: Protein | Mass: 96405.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5SX39 |
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-Tropomyosin, alpha-1 ... , 3 types, 4 molecules HIJK
#4: Protein | Mass: 9975.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#5: Protein | Mass: 10060.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#6: Protein | Mass: 7507.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
-Non-polymers , 2 types, 10 molecules
#8: Chemical | ChemComp-ADP / #9: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | N |
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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: Mouse psoas muscle myofibrils / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#7 / Source: NATURAL |
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Source (natural) | Organism: Mus musculus (house mouse) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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 defocus min: 2400 nm / Calibrated defocus max: 5000 nm / 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: 3.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k 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: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104302 / Symmetry type: POINT | |||||||||||||||
EM volume selection | Num. of tomograms: 48 / Num. of volumes extracted: 183260 | |||||||||||||||
Atomic model building | B value: 75 / Space: REAL Details: Mg was not refined but copied from the initial model | |||||||||||||||
Atomic model building |
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