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- EMDB-7029: CryoEM map from poorly ordered myosin thick filaments isolated fr... -

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Basic information

Entry
Database: EMDB / ID: 7029
TitleCryoEM map from poorly ordered myosin thick filaments isolated from asynchronous flight muscle of the large waterbug Lethocerus indicus
SampleLethocerus flight muscle myosin filament
SourceLethocerus indicus / arthropod
Map dataPrimary map
Methodsingle particle reconstruction, at 6.4 Å resolution
AuthorsTaylor KA / Taylor D / Hu Z / Edwards RJ
CitationJ. Struct. Biol., 2017

J. Struct. Biol., 2017 Yorodumi Papers
Coupling between myosin head conformation and the thick filament backbone structure.
Zhongjun Hu / Dianne W Taylor / Robert J Edwards / Kenneth A Taylor

DateDeposition: Sep 15, 2017 / Header (metadata) release: Oct 11, 2017 / Map release: Oct 11, 2017 / Last update: Oct 11, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_7029.map.gz (map file in CCP4 format, 322487 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
432 pix
1.22 Å/pix.
= 528.336 Å
432 pix
1.22 Å/pix.
= 528.336 Å
432 pix
1.22 Å/pix.
= 528.336 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.223 Å
Density
Contour Level:0.032 (by author), 0.012 (movie #1):
Minimum - Maximum-0.056497645 - 0.18061732
Average (Standard dev.)0.00056291226 (0.009138624)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions432432432
Origin000
Limit431431431
Spacing432432432
CellA=B=C: 1 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2231.2231.223
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z528.336528.336528.336
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0560.1810.001

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Supplemental data

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Sample components

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Entire Lethocerus flight muscle myosin filament

EntireName: Lethocerus flight muscle myosin filament / Number of components: 1

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Component #1: protein, Lethocerus flight muscle myosin filament

ProteinName: Lethocerus flight muscle myosin filament / Recombinant expression: No
SourceSpecies: Lethocerus indicus / arthropod
Source (natural)Organelle: myofibril / Organ or tissue: striated muscle

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Experimental details

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Sample preparation

Specimen statefilament
Sample solutionpH: 6.8
Support filmGatan Solarus 950.M plasma cleaner
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: All data collection details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 65 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionDetails: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 50000
Details: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
3D reconstructionSoftware: RELION
CTF correction: All specimen and sample preparation details may be found in Z. Hu, D. W. Taylor, M. K. Reedy, R. J. Edwards, K. A. Taylor, Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Angstrom resolution. Sci. Adv. 2, e1600058 (2016). Can also be found in the Specimen section of EMD-3301
Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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