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- PDB-6kn8: Structure of human cardiac thin filament in the calcium bound state -

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Basic information

Entry
Database: PDB / ID: 6kn8
TitleStructure of human cardiac thin filament in the calcium bound state
Components
  • (Tropomyosin alpha-1 ...) x 2
  • Actin, alpha skeletal muscle
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
  • Troponin T, cardiac muscle
KeywordsCONTRACTILE PROTEIN/ACTIN BINDING PROTEIN / Troponin / 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 Troponin complex / cardiac myofibril ...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 Troponin complex / cardiac myofibril / bleb / 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 / ruffle organization / 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 / myosin heavy chain binding / ventricular cardiac muscle tissue morphogenesis / heart contraction / tropomyosin binding / regulation of heart contraction / negative regulation of vascular associated smooth muscle cell migration / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / negative regulation of vascular associated smooth muscle cell proliferation / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / Smooth Muscle Contraction / skeletal muscle contraction / vasculogenesis / calcium channel inhibitor activity / cytoskeletal protein binding / skeletal muscle fiber development / cardiac muscle contraction / stress fiber / Ion homeostasis / positive regulation of stress fiber assembly / titin binding / actin filament polymerization / cytoskeleton organization / positive regulation of cell adhesion / actin filament organization / negative regulation of cell migration / sarcomere / cellular response to reactive oxygen species / filopodium / actin filament / wound healing / response to calcium ion / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / regulation of cell shape / lamellipodium / actin cytoskeleton / heart development / actin binding / cell body / cytoskeleton / hydrolase activity / protein heterodimerization activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / protein kinase binding / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm / cytosol
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 / EF-Hand 1, calcium-binding site / ATPase, nucleotide binding domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 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 speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsFujii, T. / Yamada, Y. / Namba, K.
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, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
K: Actin, alpha skeletal muscle
L: Actin, alpha skeletal muscle
M: Actin, alpha skeletal muscle
N: Actin, alpha skeletal muscle
O: Actin, alpha skeletal muscle
P: Tropomyosin alpha-1 chain
Q: Tropomyosin alpha-1 chain
R: Tropomyosin alpha-1 chain
S: Tropomyosin alpha-1 chain
T: Troponin T, cardiac muscle
U: Troponin I, cardiac muscle
V: Troponin C, slow skeletal and cardiac muscles
W: Tropomyosin alpha-1 chain
X: Tropomyosin alpha-1 chain
Y: Tropomyosin alpha-1 chain
Z: Tropomyosin alpha-1 chain
a: Troponin T, cardiac muscle
b: Troponin I, cardiac muscle
c: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)883,01044
Polymers876,60229
Non-polymers6,40815
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area129930 Å2
ΔGint-847 kcal/mol
Surface area308970 Å2

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Components

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Protein , 4 types, 21 molecules ABCDEFGHIJKLMNOTaUbVc

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#4: Protein Troponin T, cardiac muscle / TnTc / Cardiac muscle troponin T / cTnT


Mass: 21446.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNT2 / Production host: Escherichia coli (E. coli) / References: UniProt: P45379
#5: Protein Troponin I, cardiac muscle / Cardiac troponin I


Mass: 14430.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3, TNNC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19429
#6: Protein Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 18288.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC / Production host: Escherichia coli (E. coli) / References: UniProt: P63316

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Tropomyosin alpha-1 ... , 2 types, 8 molecules PQWXRSYZ

#2: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 31555.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPM1, C15orf13, TMSA / Production host: Escherichia coli (E. coli) / References: UniProt: P09493
#3: Protein/peptide
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 3528.104 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPM1, C15orf13, TMSA / Production host: Escherichia coli (E. coli) / References: UniProt: P09493

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Non-polymers , 1 types, 15 molecules

#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1Cardiac muscle thin filament in the calcium bound stateCOMPLEX#1-#60RECOMBINANT
2Actin, alpha skeletal muscleCOMPLEX#11NATURAL
3Tropomyosin, TroponinCOMPLEX#2-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Oryctolagus cuniculus (rabbit)9986
31Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23374 / Symmetry type: POINT

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