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- EMDB-0728: Structure of human cardiac thin filament in the calcium free state -

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Basic information

Entry
Database: EMDB / ID: EMD-0728
TitleStructure of human cardiac thin filament in the calcium free state
Map data
Sample
  • Complex: Cardiac muscle thin filament in the calcium free state
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Tropomyosin, Troponin
      • Protein or peptide: Tropomyosin alpha-1 chain
      • Protein or peptide: Tropomyosin alpha-1 chain
      • Protein or peptide: Troponin T, cardiac muscle
      • Protein or peptide: Troponin I, cardiac muscle
      • Protein or peptide: Troponin C, slow skeletal and cardiac muscles
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsTroponin / Tropomyosin / Actin / Thin filement / Muscle / CONTRACTILE PROTEIN-ACTIN BINDING PROTEIN complex
Function / homology
Function and homology information


positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex ...positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex / bleb / troponin complex / regulation of muscle contraction / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / ruffle organization / positive regulation of ATP-dependent activity / Striated Muscle Contraction / muscle filament sliding / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / structural constituent of muscle / sarcomere organization / cytoskeletal motor activator activity / ventricular cardiac muscle tissue morphogenesis / myosin heavy chain binding / heart contraction / regulation of heart contraction / tropomyosin binding / negative regulation of vascular associated smooth muscle cell migration / troponin I binding / filamentous actin / mesenchyme migration / negative regulation of vascular associated smooth muscle cell proliferation / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / Smooth Muscle Contraction / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / stress fiber / skeletal muscle fiber development / Ion homeostasis / cytoskeletal protein binding / cardiac muscle contraction / positive regulation of stress fiber assembly / titin binding / actin filament polymerization / cytoskeleton organization / positive regulation of cell adhesion / negative regulation of cell migration / sarcomere / actin filament organization / filopodium / cellular response to reactive oxygen species / actin filament / wound healing / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / ruffle membrane / intracellular calcium ion homeostasis / response to calcium ion / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / regulation of cell shape / actin binding / heart development / cell body / cytoskeleton / hydrolase activity / protein domain specific binding / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin ...Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin / EF-hand domain pair / Actins signature 1. / : / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding 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
Similarity search - Domain/homology
Tropomyosin alpha-1 chain / Troponin I, cardiac muscle / Troponin T, cardiac muscle / Troponin C, slow skeletal and cardiac muscles / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsFujii T / Yamada Y
CitationJournal: Nat Commun / Year: 2020
Title: Cardiac muscle thin filament structures reveal calcium regulatory mechanism.
Authors: Yurika Yamada / Keiichi Namba / Takashi Fujii /
Abstract: Contraction of striated muscles is driven by cyclic interactions of myosin head projecting from the thick filament with actin filament and is regulated by Ca released from sarcoplasmic reticulum. ...Contraction of striated muscles is driven by cyclic interactions of myosin head projecting from the thick filament with actin filament and is regulated by Ca released from sarcoplasmic reticulum. Muscle thin filament consists of actin, tropomyosin and troponin, and Ca binding to troponin triggers conformational changes of troponin and tropomyosin to allow actin-myosin interactions. However, the structural changes involved in this regulatory mechanism remain unknown. Here we report the structures of human cardiac muscle thin filament in the absence and presence of Ca by electron cryomicroscopy. Molecular models in the two states built based on available crystal structures reveal the structures of a C-terminal region of troponin I and an N-terminal region of troponin T in complex with the head-to-tail junction of tropomyosin together with the troponin core on actin filament. Structural changes of the thin filament upon Ca binding now reveal the mechanism of Ca regulation of muscle contraction.
History
DepositionAug 3, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0476
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0476
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kn7
  • Surface level: 0.0476
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0728.png

Downloads & links

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Map

FileDownload / File: emd_0728.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.22 Å/pix.
x 200 pix.
= 444. Å		2.22 Å/pix.
x 200 pix.
= 444. Å		2.22 Å/pix.
x 200 pix.
= 444. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0376 / Movie #1: 0.0476
Minimum - Maximum-0.071018465 - 0.22550805
Average (Standard dev.)-0.000039149214 (±0.011095973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.222.222.22
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z444.000444.000444.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0710.226-0.000

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Supplemental data

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Sample components

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Entire : Cardiac muscle thin filament in the calcium free state

EntireName: Cardiac muscle thin filament in the calcium free state
Components
  • Complex: Cardiac muscle thin filament in the calcium free state
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Tropomyosin, Troponin
      • Protein or peptide: Tropomyosin alpha-1 chain
      • Protein or peptide: Tropomyosin alpha-1 chain
      • Protein or peptide: Troponin T, cardiac muscle
      • Protein or peptide: Troponin I, cardiac muscle
      • Protein or peptide: Troponin C, slow skeletal and cardiac muscles
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cardiac muscle thin filament in the calcium free state

SupramoleculeName: Cardiac muscle thin filament in the calcium free state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #2: Actin, alpha skeletal muscle

SupramoleculeName: Actin, alpha skeletal muscle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: Tropomyosin, Troponin

SupramoleculeName: Tropomyosin, Troponin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#6

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.862613 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIITNWD DMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSGDGV T HNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.555053 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLNR RIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD RKYEEVARKL V IIESDLER ...String:
LKLDKENALD RAEQAEADKK AAEDRSKQLE DELVSLQKKL KGTEDELDKY SEALKDAQEK LELAEKKATD AEADVASLNR RIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD RKYEEVARKL V IIESDLER AEERAELSEG KCAELEEELK TVTNNLKSLE AQAEKYSQKE DRYEEEIKVL SDKLKEAETR AEFAERSVTK LE KSIDDLE DELYAQKLKY KAISEELDHA LNDMTSI

UniProtKB: Tropomyosin alpha-1 chain

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Macromolecule #3: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.528104 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ASMDAIKKKM QMLKLDKENA LDRAEQAEAD K

UniProtKB: Tropomyosin alpha-1 chain

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Macromolecule #4: Troponin T, cardiac muscle

MacromoleculeName: Troponin T, cardiac muscle / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.023039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
FDDIHRKRME KDLNELQALI EAHFENRKKE EEELVSLKDR IERRRAERAE QQRIRNEREK ERQNRLAEER ARREEEENRR KAEDEARKK KALSNMMHFG GYIQKQAQTE RKSGKRQTER EKKKKILAER RKVLAIDHLN EDQLREKAKE LWQSIYNLEA E KFDLQEKF KQQKYEINVL RNRINDNQ

UniProtKB: Troponin T, cardiac muscle

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Macromolecule #5: Troponin I, cardiac muscle

MacromoleculeName: Troponin I, cardiac muscle / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.639691 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ISASRKLQLK TLLLQIAKQE LEREAEERRG EKGRALSTRC QPLELAGLGF AELQDLCRQL HARVDKVDEE RYDIEAKVTK NITEIADLT QKIFDLRGKF KRPTLRRVRI SADAMMQALL GARAKESLDL RAHLKQVKKE DTEKENREVG DWRKNIDALS G MEGRKKKF ES

UniProtKB: Troponin I, cardiac muscle

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Macromolecule #6: Troponin C, slow skeletal and cardiac muscles

MacromoleculeName: Troponin C, slow skeletal and cardiac muscles / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.288287 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DDIYKAAVEQ LTEEQKNEFK AAFDIFVLGA EDGCISTKEL GKVMRMLGQN PTPEELQEMI DEVDEDGSGT VDFDEFLVMM VRCMKDDSK GKSEEELSDL FRMFDKNADG YIDLDELKIM LQATGETITE DDIEELMKDG DKNNDGRIDY DEFLEFMKGV E

UniProtKB: Troponin C, slow skeletal and cardiac muscles

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 15 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: OTHER / Details: EM map of actin filament
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21588
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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