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

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Basic information

Entry
Database: PDB / ID: 6klt
TitleTroponin of cardiac thin filament in low-calcium state
Components
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
  • Troponin T, cardiac muscle
KeywordsCONTRACTILE PROTEIN / Cardiac thin filament
Function / homology
Function and homology information


atrial cardiac muscle tissue morphogenesis / regulation of systemic arterial blood pressure by ischemic conditions / Striated Muscle Contraction / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / cardiac myofibril ...atrial cardiac muscle tissue morphogenesis / regulation of systemic arterial blood pressure by ischemic conditions / Striated Muscle Contraction / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / cardiac myofibril / troponin complex / regulation of muscle contraction / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / positive regulation of ATP-dependent activity / Ion homeostasis / muscle filament sliding / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / tropomyosin binding / regulation of heart contraction / troponin I binding / myofibril / striated muscle thin filament / sarcoplasm / vasculogenesis / striated muscle contraction / calcium channel inhibitor activity / cardiac muscle contraction / muscle contraction / sarcomere / response to bacterium / response to calcium ion / structural constituent of cytoskeleton / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / heart development / actin binding / protein domain specific binding / calcium ion 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsOda, T. / Yanagisawa, H. / Wakabayashi, T.
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 11, 2020Group: Data collection / Database references / Category: citation / em_imaging_optics
Item: _citation.journal_volume / _em_imaging_optics.phase_plate
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

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Assembly

Deposited unit
A: Troponin C, slow skeletal and cardiac muscles
B: Troponin T, cardiac muscle
C: Troponin I, cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9845
Polymers38,9043
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5700 Å2
ΔGint-69 kcal/mol
Surface area21900 Å2

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Components

#1: Protein Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 16644.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19123
#2: Protein Troponin T, cardiac muscle / TnTc / Cardiac muscle troponin T / cTnT


Mass: 8735.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P50752
#3: Protein Troponin I, cardiac muscle / Cardiac troponin I


Mass: 13524.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P48787
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Sequence detailsResidue GLU 32 could not be modeled due to low resolution.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: F-actin of cardiac thin filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse) / Strain: ICR / Organ: heart
Buffer solutionpH: 7.2
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: 1100 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.6 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.18CTF correction
7UCSF Chimera1.13.1model fitting
10RELION3.0.6initial Euler assignment
11RELION3.0.6final Euler assignment
12RELION3.0.6classification
13RELION3.0.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 12 Å / Resolution method: OTHER / Num. of particles: 515775
Details: Resolution was estimated based on the comparison between the map and the model-derived map.
Symmetry type: POINT
Atomic model buildingPDB-ID: 4Y99

4y99


Accession code: 4Y99 / Source name: PDB / Type: experimental model

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