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- EMDB-0717: Troponin of cardiac thin filament in low-calcium state -

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Basic information

Entry
Database: EMDB / ID: EMD-0717
TitleTroponin of cardiac thin filament in low-calcium state
Map dataCardiac troponin in low-calcium state
Sample
  • Organelle or cellular component: F-actin of cardiac thin filament
    • Protein or peptide: Troponin C, slow skeletal and cardiac muscles
    • Protein or peptide: Troponin T, cardiac muscle
    • Protein or peptide: Troponin I, cardiac muscle
  • Ligand: CALCIUM ION
KeywordsCardiac thin filament / CONTRACTILE PROTEIN
Function / homology
Function and homology information


atrial cardiac muscle tissue morphogenesis / Striated Muscle Contraction / regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / contractile muscle fiber / cardiac myofibril ...atrial cardiac muscle tissue morphogenesis / Striated Muscle Contraction / regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / contractile muscle fiber / cardiac myofibril / cardiac Troponin complex / actin crosslink formation / troponin complex / regulation of smooth muscle contraction / regulation of muscle contraction / muscle filament sliding / transition between fast and slow fiber / negative regulation of ATP-dependent activity / Ion homeostasis / positive regulation of ATP-dependent activity / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / regulation of heart contraction / myofibril / tropomyosin binding / troponin I binding / striated muscle thin filament / skeletal muscle contraction / sarcoplasm / vasculogenesis / calcium channel inhibitor activity / cardiac muscle contraction / striated muscle contraction / muscle contraction / sarcomere / response to bacterium / structural constituent of cytoskeleton / intracellular calcium ion homeostasis / response to calcium ion / calcium-dependent protein binding / actin filament binding / heart development / actin binding / protein-macromolecule adaptor activity / protein domain specific binding / calcium ion binding / protein-containing complex binding / protein kinase binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / : / EF-hand domain pair ...Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / : / EF-hand domain pair / 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
Similarity search - Domain/homology
Troponin C, slow skeletal and cardiac muscles / Troponin I, cardiac muscle / Troponin T, cardiac muscle
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsOda T / Yanagisawa H
CitationJournal: J Struct Biol / Year: 2020
Title: Cryo-EM structures of cardiac thin filaments reveal the 3D architecture of troponin.
Authors: Toshiyuki Oda / Haruaki Yanagisawa / Takeyuki Wakabayashi /
Abstract: Troponin is an essential component of striated muscle and it regulates the sliding of actomyosin system in a calcium-dependent manner. Despite its importance, the structure of troponin has been ...Troponin is an essential component of striated muscle and it regulates the sliding of actomyosin system in a calcium-dependent manner. Despite its importance, the structure of troponin has been elusive due to its high structural heterogeneity. In this study, we analyzed the 3D structures of murine cardiac thin filaments using a cryo-electron microscope equipped with a Volta phase plate (VPP). Contrast enhancement by a VPP enabled us to reconstruct the entire repeat of the thin filament. We determined the orientation of troponin relative to F-actin and tropomyosin, and characterized the interactions between troponin and tropomyosin. This study provides a structural basis for understanding the molecular mechanism of actomyosin system.
History
DepositionJul 30, 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: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.009
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  • Surface view with fitted model
  • Atomic models: PDB-6klt
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0717.png

Downloads & links

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Map

FileDownload / File: emd_0717.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCardiac troponin in low-calcium state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 264 pix.
= 282.48 Å		1.07 Å/pix.
x 264 pix.
= 282.48 Å		1.07 Å/pix.
x 264 pix.
= 282.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.022786971 - 0.07064712
Average (Standard dev.)-0.0002094979 (±0.00094411225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 282.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z282.480282.480282.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.0230.071-0.000

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Supplemental data

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Sample components

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Entire : F-actin of cardiac thin filament

EntireName: F-actin of cardiac thin filament
Components
  • Organelle or cellular component: F-actin of cardiac thin filament
    • Protein or peptide: Troponin C, slow skeletal and cardiac muscles
    • Protein or peptide: Troponin T, cardiac muscle
    • Protein or peptide: Troponin I, cardiac muscle
  • Ligand: CALCIUM ION

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Supramolecule #1: F-actin of cardiac thin filament

SupramoleculeName: F-actin of cardiac thin filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse) / Strain: ICR / Organ: heart

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Macromolecule #1: Troponin C, slow skeletal and cardiac muscles

MacromoleculeName: Troponin C, slow skeletal and cardiac muscles / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 16.644533 KDa
SequenceString:
TEEQKNEFKA AFDIFVLGAD GCISTKELGK VMRMLGQNPT PEELQEMIDE VDEDGSGTVD FDEFLVMMVR CMKDDSKGKS EEELSDLFR MFDKNADGYI DLDELKMMLQ ATGETITEDD IEELMKDGDK NNDGRIDYDE FLEFMK

UniProtKB: Troponin C, slow skeletal and cardiac muscles

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Macromolecule #2: Troponin T, cardiac muscle

MacromoleculeName: Troponin T, cardiac muscle / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 8.735045 KDa
SequenceString:
GKRQTEREKK KKILAERRKA LAIDHLNEDQ LREKAKELWQ SIHNLEAEKF DLQEKFKQQK YEINVLRNRI N

UniProtKB: Troponin T, cardiac muscle

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Macromolecule #3: Troponin I, cardiac muscle

MacromoleculeName: Troponin I, cardiac muscle / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.524673 KDa
SequenceString:
QLKTLMLQIA KQEMEREAEE RRGEKGRVLR TRCQPLELDG LGFEELQDLC RQLHARVDKV DEERYDVEAK VTKNITEIAD LTQKIYDLR GKFKRPTLRR VRISADAMMQ ALLGTR

UniProtKB: Troponin I, cardiac muscle

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration0.1 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

7938

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3.0.6)
Details: Resolution was estimated based on the comparison between the map and the model-derived map.
Number images used: 515775
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.6)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4y99


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6klt:
Troponin of cardiac thin filament in low-calcium state

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