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Yorodumi- PDB-6kn7: Structure of human cardiac thin filament in the calcium free state -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kn7 | ||||||
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Title | Structure of human cardiac thin filament in the calcium free state | ||||||
Components |
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Keywords | CONTRACTILE 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 / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / 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 / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / troponin complex / bleb / negative regulation of vascular associated smooth muscle cell migration / regulation of smooth muscle contraction / regulation of muscle contraction / muscle filament sliding / transition between fast and slow fiber / negative regulation of ATP-dependent activity / ruffle organization / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of ATP-dependent activity / Striated Muscle Contraction / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / cytoskeletal motor activator activity / regulation of heart contraction / sarcomere organization / tropomyosin binding / heart contraction / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle contraction / skeletal muscle myofibril / positive regulation of cell adhesion / actin monomer binding / Smooth Muscle Contraction / vasculogenesis / calcium channel inhibitor activity / skeletal muscle fiber development / cardiac muscle contraction / stress fiber / Ion homeostasis / titin binding / positive regulation of stress fiber assembly / cytoskeleton organization / cytoskeletal protein binding / actin filament polymerization / sarcomere / negative regulation of cell migration / filopodium / actin filament organization / actin filament / ruffle membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / wound healing / cellular response to reactive oxygen species / response to calcium ion / structural constituent of cytoskeleton / actin filament binding / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin cytoskeleton / lamellipodium / heart development / actin binding / regulation of cell shape / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å | ||||||
Authors | Fujii, T. / Yamada, Y. / Namba, K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6kn7.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6kn7.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6kn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kn7_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6kn7_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6kn7_validation.xml.gz | 195.1 KB | Display | |
Data in CIF | 6kn7_validation.cif.gz | 300.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/6kn7 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/6kn7 | HTTPS FTP |
-Related structure data
Related structure data | 0728MC 0729C 6kn8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 21 molecules ABCDEFGHIJKLMNOTaUbVc
#1: Protein | 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 | Mass: 23023.039 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 | Mass: 19639.691 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 | 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 | 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 | 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 / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 200 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21588 / Symmetry type: POINT |