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- PDB-8q6t: Helical reconstruction of the relaxed thick filament from FIB mil... -

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Basic information

Entry
Database: PDB / ID: 8q6t
TitleHelical reconstruction of the relaxed thick filament from FIB milled left ventricular mouse myofibrils
Components
  • Myosin binding protein C, cardiac
  • Myosin light chain 3
  • Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
  • Myosin-7
  • Titin
KeywordsMOTOR PROTEIN / Mammalian / Muscle / Thick filament / Cardiac
Function / homology
Function and homology information


heart growth / forward locomotion / striated muscle cell development / regulation of relaxation of cardiac muscle / muscle cell fate specification / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / Striated Muscle Contraction / regulation of striated muscle contraction / detection of muscle stretch ...heart growth / forward locomotion / striated muscle cell development / regulation of relaxation of cardiac muscle / muscle cell fate specification / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / Striated Muscle Contraction / regulation of striated muscle contraction / detection of muscle stretch / muscle myosin complex / ventricular system development / cardiac myofibril assembly / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / muscle cell development / adult heart development / cardiac muscle tissue morphogenesis / cardiac muscle hypertrophy in response to stress / muscle filament sliding / M band / myosin complex / A band / I band / structural constituent of muscle / ankyrin binding / sarcomere organization / intracellular membraneless organelle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / heart contraction / positive regulation of the force of heart contraction / myofibril / actin monomer binding / skeletal muscle contraction / somitogenesis / ATP metabolic process / heart morphogenesis / stress fiber / cardiac muscle contraction / muscle contraction / regulation of heart rate / sarcomere / post-embryonic development / structural constituent of cytoskeleton / Z disc / actin filament binding / actin binding / heart development / protein tyrosine kinase activity / in utero embryonic development / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / calmodulin binding / cell adhesion / protein serine kinase activity / calcium ion binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
PPAK motif / : / PPAK motif / Titin, Z repeat / Titin Z / : / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail ...PPAK motif / : / PPAK motif / Titin, Z repeat / Titin Z / : / MyBP-C, tri-helix bundle domain / Tri-helix bundle 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 head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / Kinesin motor domain superfamily / : / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / EF-hand domain pair / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / EF-hand, calcium binding motif / Immunoglobulin V-set domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Titin / Myosin light chain 3 / Myosin regulatory light chain 2, ventricular/cardiac muscle isoform / Myosin binding protein C, cardiac / Myosin-7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 18 Å
AuthorsTamborrini, D. / Raunser, S.
Funding support Germany, European Union, United Kingdom, 5items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)856118European Union
Wellcome Trust201543/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R003106/1 United Kingdom
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Nature / Year: 2023
Title: Structure of the native myosin filament in the relaxed cardiac sarcomere.
Authors: Davide Tamborrini / Zhexin Wang / Thorsten Wagner / Sebastian Tacke / Markus Stabrin / Michael Grange / Ay Lin Kho / Martin Rees / Pauline Bennett / Mathias Gautel / Stefan Raunser /
Abstract: The thick filament is a key component of sarcomeres, the basic units of striated muscle. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other ...The thick filament is a key component of sarcomeres, the basic units of striated muscle. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other heart and muscle diseases. Despite the central importance of the thick filament, its molecular organization remains unclear. Here we present the molecular architecture of native cardiac sarcomeres in the relaxed state, determined by cryo-electron tomography. Our reconstruction of the thick filament reveals the three-dimensional organization of myosin, titin and myosin-binding protein C (MyBP-C). The arrangement of myosin molecules is dependent on their position along the filament, suggesting specialized capacities in terms of strain susceptibility and force generation. Three pairs of titin-α and titin-β chains run axially along the filament, intertwining with myosin tails and probably orchestrating the length-dependent activation of the sarcomere. Notably, whereas the three titin-α chains run along the entire length of the thick filament, titin-β chains do not. The structure also demonstrates that MyBP-C bridges thin and thick filaments, with its carboxy-terminal region binding to the myosin tails and directly stabilizing the OFF state of the myosin heads in an unforeseen manner. These results provide a foundation for future research investigating muscle disorders involving sarcomeric components.
History
DepositionAug 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-7
B: Myosin-7
C: Myosin light chain 3
D: Myosin light chain 3
E: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
F: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
G: Myosin binding protein C, cardiac
H: Myosin-7
I: Titin
J: Myosin light chain 3
K: Myosin light chain 3
L: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
M: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
N: Myosin-7
O: Myosin-7
P: Titin
Q: Myosin-7
R: Myosin light chain 3
S: Myosin light chain 3
T: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
U: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
V: Myosin binding protein C, cardiac


Theoretical massNumber of molelcules
Total (without water)1,879,46422
Polymers1,879,46422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Myosin-7 / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac ...Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta


Mass: 223226.531 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91Z83
#2: Protein
Myosin light chain 3


Mass: 17243.553 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P09542
#3: Protein
Myosin regulatory light chain 2, ventricular/cardiac muscle isoform


Mass: 18259.512 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P51667
#4: Protein Myosin binding protein C, cardiac


Mass: 44777.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3TF37
#5: Protein Titin


Mass: 118766.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2ASS6
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Relaxed thick filament; A-band region; C-type super-repeat
Type: CELL
Details: Single asymmetrical unit from the relaxed thick filament obtained from FIB milled left ventricular mouse myofibrils
Entity ID: #1-#3, #5, #4 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 6000 nm / Nominal defocus min: 3000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.4 e/Å2 / Avg electron dose per subtomogram: 140 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
4WarpCTF correction
5RELIONCTF correction
8NAMDmodel fitting
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0 ° / Axial rise/subunit: 430 Å / Axial symmetry: C3
3D reconstructionResolution: 18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1589
Details: Helical reconstruction containing 4.5x repeats extrapolated from a 3x repeat reconstruction (EMD-18146)
Symmetry type: HELICAL
EM volume selectionNum. of tomograms: 89 / Num. of volumes extracted: 67492
Atomic model building
ID 3D fitting-IDSource name
11AlphaFold
21SwissModel

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