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- PDB-7qim: In situ structure of nebulin bound to actin filament in skeletal ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qim | ||||||||||||||||||
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Title | In situ structure of nebulin bound to actin filament in skeletal sarcomere | ||||||||||||||||||
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![]() | CONTRACTILE PROTEIN / Skeletal muscle / Sarcomere / Thin filament | ||||||||||||||||||
Function / homology | ![]() Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain Similarity search - Domain/homology | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.5 Å | ||||||||||||||||||
![]() | Wang, Z. / Grange, M. / Pospich, S. / Wagner, T. / Kho, A.L. / Gautel, M. / Raunser, S. | ||||||||||||||||||
Funding support | European Union, 5items
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 334.9 KB | Display | ![]() |
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PDB format | ![]() | 285.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 64 KB | Display | |
Data in CIF | ![]() | 88 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13990MC ![]() 7qinC ![]() 7qioC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 42109.973 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | | Mass: 9188.235 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 6131.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-MG / 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 |
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Sample preparation
Component | Name: Mouse psoas muscle myofibrils / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
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 |
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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: ![]() |
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) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141860 / Symmetry type: POINT | |||||||||||||||
EM volume selection | Num. of tomograms: 48 / Num. of volumes extracted: 183260 | |||||||||||||||
Atomic model building | B value: 100 / Space: REAL Details: Mg was not refined but copied from the initial model | |||||||||||||||
Atomic model building | PDB-ID: 5JLH Pdb chain-ID: A |