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- PDB-6kln: F-actin of cardiac thin filament in high-calcium state -

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Basic information

Entry
Database: PDB / ID: 6kln
TitleF-actin of cardiac thin filament in high-calcium state
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / Cardiac thin filament
Function / homology
Function and homology information


Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / hydrolase activity / positive regulation of gene expression / protein-containing complex / ATP binding / cytoplasm
Similarity search - Function
ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain ...ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 1.0Jan 15, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jan 15, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 15, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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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 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
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Revision 1.1Apr 9, 2025Data content type: EM metadata
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Group: Data processing / Database references ...Data processing / Database references / Experimental summary / Refinement description
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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 / _em_admin.last_update

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,30912
Polymers167,5034
Non-polymers1,8068
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11250 Å2
ΔGint-118 kcal/mol
Surface area58110 Å2

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Components

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


Mass: 41875.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: Heart / References: UniProt: P68134
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN
Has protein modificationY

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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: Cardiac thin filament / Type: COMPLEX / Entity ID: #1 / 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
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 / Nominal defocus min: 100 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

SoftwareName: PHENIX / Version: 1.15_3459: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.0.6particle selection
4Gctf1.18CTF correction
7PHENIX1.15-3459model fitting
9RELION3.0.6initial Euler assignment
10RELION3.0.6final Euler assignment
11RELION3.0.6classification
12RELION3.0.63D reconstruction
13PHENIX1.15-3459model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255620 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6DJO

6djo


Accession code: 6DJO / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00912004
ELECTRON MICROSCOPYf_angle_d0.77516292
ELECTRON MICROSCOPYf_dihedral_angle_d17.2897220
ELECTRON MICROSCOPYf_chiral_restr0.0531808
ELECTRON MICROSCOPYf_plane_restr0.0042084

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