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- PDB-6kll: F-actin of cardiac thin filament in low-calcium state -

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Basic information

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


skeletal muscle fiber adaptation / Striated Muscle Contraction / cellular response to potassium ion / response to steroid hormone / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / response to mechanical stimulus / stress fiber / skeletal muscle fiber development ...skeletal muscle fiber adaptation / Striated Muscle Contraction / cellular response to potassium ion / response to steroid hormone / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / response to mechanical stimulus / stress fiber / skeletal muscle fiber development / 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
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
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 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

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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 area11170 Å2
ΔGint-115 kcal/mol
Surface area58770 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

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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 / Tissue: 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 Bioquantum / 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 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 515775 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6DJO

6djo

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00712004
ELECTRON MICROSCOPYf_angle_d0.69716292
ELECTRON MICROSCOPYf_dihedral_angle_d16.3537220
ELECTRON MICROSCOPYf_chiral_restr0.0521808
ELECTRON MICROSCOPYf_plane_restr0.0042084

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