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- EMDB-18147: Thin filament from FIB milled relaxed left ventricular mouse myof... -

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Basic information

Entry
Database: EMDB / ID: EMD-18147
TitleThin filament from FIB milled relaxed left ventricular mouse myofibrilsMyofilament
Map dataComposite map (EMD-16986 and EMD-16987) for the thin filament in relaxed ventricular mouse myofibrils. Enhanced with LocSpiral.
Sample
  • Tissue: Calcium-free thin filament from relaxed mouse left-ventricular myofibrils
    • Protein or peptide: Tropomyosin alpha-1 chain
    • Protein or peptide: Actin, alpha cardiac muscle 1
Keywordsmuscle sarcomere calcium-free cardiac thin-filament / STRUCTURAL PROTEIN
Function / homology
Function and homology information


actin-mediated cell contraction / RHOB GTPase cycle / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Striated Muscle Contraction / RHOA GTPase cycle / Smooth Muscle Contraction / actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly ...actin-mediated cell contraction / RHOB GTPase cycle / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / Striated Muscle Contraction / RHOA GTPase cycle / Smooth Muscle Contraction / actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / muscle filament sliding / cardiac muscle tissue morphogenesis / actin filament capping / ruffle organization / actomyosin structure organization / I band / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myosin binding / myofibril / heart contraction / mesenchyme migration / skeletal muscle thin filament assembly / positive regulation of cell adhesion / cardiac muscle contraction / positive regulation of stress fiber assembly / sarcomere / negative regulation of cell migration / filopodium / actin filament / actin filament organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / wound healing / structural constituent of cytoskeleton / disordered domain specific binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / actin binding / response to ethanol / in utero embryonic development / hydrolase activity / response to xenobiotic stimulus / protein heterodimerization activity / synapse / glutamatergic synapse / positive regulation of gene expression / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Tropomyosins signature. / Tropomyosin / Tropomyosin / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...Tropomyosins signature. / Tropomyosin / Tropomyosin / 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
Tropomyosin alpha-1 chain / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 8.0 Å
AuthorsTamborrini D / Wang Z / Wagner T / Tacke S / Stabrin M / Grange M / Kho AL / Bennet P / Rees M / Gautel M / Raunser S
Funding supportEuropean Union, Canada, 3 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)European Union
Medical Research Council (MRC, Canada)MR/R003106/1 Canada
European Research Council (ERC)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 6, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18147.png

Downloads & links

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Map

FileDownload / File: emd_18147.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map (EMD-16986 and EMD-16987) for the thin filament in relaxed ventricular mouse myofibrils. Enhanced with LocSpiral.
Voxel sizeX=Y=Z: 2.293 Å
Density
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-0.0010494398 - 0.9529556
Average (Standard dev.)0.02058492 (±0.09611519)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 293.504 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Calcium-free thin filament from relaxed mouse left-ventricular my...

EntireName: Calcium-free thin filament from relaxed mouse left-ventricular myofibrils
Components
  • Tissue: Calcium-free thin filament from relaxed mouse left-ventricular myofibrils
    • Protein or peptide: Tropomyosin alpha-1 chain
    • Protein or peptide: Actin, alpha cardiac muscle 1

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Supramolecule #1: Calcium-free thin filament from relaxed mouse left-ventricular my...

SupramoleculeName: Calcium-free thin filament from relaxed mouse left-ventricular myofibrils
type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Mus musculus (house mouse) / Organ: Heart / Tissue: left-ventricular muscle

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Macromolecule #1: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Mus musculus (house mouse) / Organ: HEART / Tissue: left-ventricular muscle
Molecular weightTheoretical: 41.471258 KDa
SequenceString: ETTALVCDNG SGLVKAGFAG DDAPRAVFPS IVGRPRHQGV MVGMGQKDSY VGDEAQSKRG ILTLKYPIEH GIITNWDDME KIWHHTFYN ELRVAPEEHP TLLTEAPLNP KANREKMTQI MFETFNVPAM YVAIQAVLSL YASGRTTGIV LDSGDGVTHN V PIYEGYAL ...String:
ETTALVCDNG SGLVKAGFAG DDAPRAVFPS IVGRPRHQGV MVGMGQKDSY VGDEAQSKRG ILTLKYPIEH GIITNWDDME KIWHHTFYN ELRVAPEEHP TLLTEAPLNP KANREKMTQI MFETFNVPAM YVAIQAVLSL YASGRTTGIV LDSGDGVTHN V PIYEGYAL PHAIMRLDLA GRDLTDYLMK ILTERGYSFV TTAEREIVRD IKEKLCYVAL DFENEMATAA SSSSLEKSYE LP DGQVITI GNERFRCPET LFQPSFIGME SAGIHETTYN SIMKCDIDIR KDLYANNVLS GGTTMYPGIA DRMQKEITAL APS TMKIKI IAPPERKYSV WIGGSILASL STFQQMWISK QEYDEAGPSI VHRKCF

UniProtKB: Actin, alpha cardiac muscle 1

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Macromolecule #2: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Organ: HEART / Tissue: left-ventricular muscle
Molecular weightTheoretical: 20.840275 KDa
SequenceString:
IQLVEEELDR AQERLATALQ KLEEAEKAAD ESERGMKVIE SRAQKDEEKM EIQEIQLKEA KHIAEDADRK YEEVARKLVI IESDLERAE ERAELSEGKC AELEEELKTV TNNLKSLEAQ AEKYSQKEDK YEEEIKVLSD KLKEAETRAE FAERSVTKLE K SIDDLEDE LYAQKLKYKA I

UniProtKB: Tropomyosin alpha-1 chain

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 89 / Number images used: 365971 / Software - Name: Warp
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 100447

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8q4g:
Thin filament from FIB milled relaxed left ventricular mouse myofibrils

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