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- PDB-7qin: In situ structure of actomyosin complex in skeletal sarcomere -

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Basic information

Entry
Database: PDB / ID: 7qin
TitleIn situ structure of actomyosin complex in skeletal sarcomere
Components
  • (nebulin (mouse)) x 2
  • (tropomyosin, alpha-1 ...) x 3
  • Actin, alpha skeletal muscle
  • Myosin-4
KeywordsCONTRACTILE PROTEIN / Skeletal muscle / Sarcomere / Thin filament / Cross-bridge
Function / homology
Function and homology information


skeletal muscle fiber adaptation / Striated Muscle Contraction / cellular response to organonitrogen compound / myosin filament / : / myosin II complex / response to steroid hormone / microfilament motor activity / myofibril / mesenchyme migration ...skeletal muscle fiber adaptation / Striated Muscle Contraction / cellular response to organonitrogen compound / myosin filament / : / myosin II complex / response to steroid hormone / 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 / sarcomere / filopodium / response to activity / muscle contraction / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / double-stranded RNA binding / lamellipodium / cell body / calmodulin binding / hydrolase activity / positive regulation of gene expression / protein-containing complex / ATP binding / cytoplasm
Similarity search - Function
DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. ...DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Actins signature 1. / Actin, conserved site / Actins signature 2. / Kinesin motor domain superfamily / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle / Myosin-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.6 Å
AuthorsWang, Z. / Grange, M. / Pospich, S. / Wagner, T. / Kho, A.L. / Gautel, M. / Raunser, S.
Funding supportEuropean Union, 5items
OrganizationGrant numberCountry
Max Planck SocietyEuropean Union
Wellcome Trust201543/Z/16/ZEuropean Union
European Research Council (ERC)856118European Union
Medical Research Council (MRC, United Kingdom)MR/R003106/1European Union
European Molecular Biology Organization (EMBO)European Union
CitationJournal: 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
DepositionDec 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: nebulin (mouse)
G: nebulin (mouse)
H: tropomyosin, alpha-1 (mouse)
I: tropomyosin, alpha-1 (mouse)
J: tropomyosin, alpha-1 (mouse)
K: tropomyosin, alpha-1 (mouse)
L: Myosin-4
M: Myosin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,37523
Polymers450,11713
Non-polymers2,25810
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 9 molecules ABCDEFGLM

#1: Protein
Actin, alpha skeletal muscle / / Alpha-actin-1


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 nebulin (mouse)


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 nebulin (mouse)


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 Myosin-4 / / Myosin heavy chain 2b / MyHC-2b / Myosin heavy chain 4


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 tropomyosin, alpha-1 (mouse) /


Mass: 9975.288 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#5: Protein tropomyosin, alpha-1 (mouse) /


Mass: 10060.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: Protein tropomyosin, alpha-1 (mouse) /


Mass: 7507.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 2 types, 10 molecules

#8: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Mouse psoas muscle myofibrils / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Calibrated defocus min: 2400 nm / Calibrated defocus max: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron 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
IDNameCategory
2SerialEMimage acquisition
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
14ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104302 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 48 / Num. of volumes extracted: 183260
Atomic model buildingB value: 75 / Space: REAL
Details: Mg was not refined but copied from the initial model
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
15JLH

5jlh

A1
23I5G

3i5g

A1

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