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- PDB-7qio: Homology model of myosin neck domain in skeletal sarcomere -

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Basic information

Entry
Database: PDB / ID: 7qio
TitleHomology model of myosin neck domain in skeletal sarcomere
Components
  • Myosin light chain 1/3, skeletal muscle isoform
  • Myosin regulatory light chain 2, skeletal muscle isoform
  • Myosin-4
KeywordsMOTOR PROTEIN / Skeletal muscle / Sarcomere / Cross-bridge
Function / homology
Function and homology information


Striated Muscle Contraction / Smooth Muscle Contraction / muscle myosin complex / myosin filament / myosin complex / structural constituent of muscle / response to muscle activity / myofibril / cytoskeletal motor activity / skeletal muscle tissue development ...Striated Muscle Contraction / Smooth Muscle Contraction / muscle myosin complex / myosin filament / myosin complex / structural constituent of muscle / response to muscle activity / myofibril / cytoskeletal motor activity / skeletal muscle tissue development / muscle contraction / actin filament binding / double-stranded RNA binding / calmodulin binding / calcium ion binding / ATP binding
Similarity search - Function
: / EF-hand domain / 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 motor domain profile. ...: / EF-hand domain / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Myosin light chain 1/3, skeletal muscle isoform / Myosin regulatory light chain 11 / Myosin-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9 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
Revision 1.2Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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  • Superimposition on EM map
  • EMDB-13993
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Myosin-4
M: Myosin-4
N: Myosin light chain 1/3, skeletal muscle isoform
O: Myosin light chain 1/3, skeletal muscle isoform
P: Myosin regulatory light chain 2, skeletal muscle isoform
Q: Myosin regulatory light chain 2, skeletal muscle isoform


Theoretical massNumber of molelcules
Total (without water)272,0096
Polymers272,0096
Non-polymers00
Water00
1
L: Myosin-4


Theoretical massNumber of molelcules
Total (without water)96,4061
Polymers96,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
M: Myosin-4


Theoretical massNumber of molelcules
Total (without water)96,4061
Polymers96,4061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
3
N: Myosin light chain 1/3, skeletal muscle isoform


Theoretical massNumber of molelcules
Total (without water)20,6201
Polymers20,6201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
4
O: Myosin light chain 1/3, skeletal muscle isoform


Theoretical massNumber of molelcules
Total (without water)20,6201
Polymers20,6201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
5
P: Myosin regulatory light chain 2, skeletal muscle isoform


Theoretical massNumber of molelcules
Total (without water)18,9781
Polymers18,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
6
Q: Myosin regulatory light chain 2, skeletal muscle isoform


Theoretical massNumber of molelcules
Total (without water)18,9781
Polymers18,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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
#2: Protein Myosin light chain 1/3, skeletal muscle isoform / MLC1/MLC3 / MLC1F/MLC3F / Myosin light chain alkali 1/2 / Myosin light chain A1/A2


Mass: 20620.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05977
#3: Protein Myosin regulatory light chain 2, skeletal muscle isoform / Fast skeletal myosin light chain 2 / MLC2F


Mass: 18978.445 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

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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: all / 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 FIELD / Nominal magnification: 81000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2400 nm / 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 / Avg electron dose per subtomogram: 130 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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44001 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 48 / Num. of volumes extracted: 183260
Atomic model buildingB value: 300 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
17QIN

7qin

L7QIN1
23I5G

3i5g

B3I5G2
33I5G

3i5g

C3I5G2

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