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- EMDB-0796: F-actin part of cardiac thin filament, actin levels II-IV, low ca... -

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Basic information

Entry
Database: EMDB / ID: EMD-0796
TitleF-actin part of cardiac thin filament, actin levels II-IV, low calcium state
Map dataF-actin part of cardiac Thin filament, actin levels II-IV, low calcium state
Sample
  • Organelle or cellular component: F-actin of cardiac thin filament
Function / homology
Function and homology information


skeletal muscle fiber adaptation / Striated Muscle Contraction / : / response to steroid hormone / mesenchyme migration / skeletal muscle thin filament assembly / striated muscle thin filament / stress fiber / skeletal muscle fiber development / response to mechanical stimulus ...skeletal muscle fiber adaptation / Striated Muscle Contraction / : / response to steroid hormone / mesenchyme migration / skeletal muscle thin filament assembly / striated muscle thin filament / stress fiber / skeletal muscle fiber development / response to mechanical stimulus / 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
Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsOda T / Yanagisawa H
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
DepositionSep 30, 2019-
Header (metadata) releaseJan 15, 2020-
Map releaseJan 15, 2020-
UpdateMar 11, 2020-
Current statusMar 11, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.024
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.024
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0796.png

Downloads & links

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Map

FileDownload / File: emd_0796.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationF-actin part of cardiac Thin filament, actin levels II-IV, low calcium state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 264 pix.
= 282.48 Å		1.07 Å/pix.
x 264 pix.
= 282.48 Å		1.07 Å/pix.
x 264 pix.
= 282.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024 / Movie #1: 0.024
Minimum - Maximum-0.012410355 - 0.061186414
Average (Standard dev.)0.0008455625 (±0.0036262153)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 282.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z282.480282.480282.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-0.0120.0610.001

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Supplemental data

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Sample components

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Entire : F-actin of cardiac thin filament

EntireName: F-actin of cardiac thin filament
Components
  • Organelle or cellular component: F-actin of cardiac thin filament

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Supramolecule #1: F-actin of cardiac thin filament

SupramoleculeName: F-actin of cardiac thin filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse) / Strain: ICR / Organ: heart

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: EMDB MAP
EMDB ID:

7938

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 471020
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.6)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4y99

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