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- EMDB-10998: Mitochondrial ATP synthase monomer from Rattus norvegicus domestica -

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Basic information

Entry
Database: EMDB / ID: EMD-10998
TitleMitochondrial ATP synthase monomer from Rattus norvegicus domestica
Map data
Sample
  • Organelle or cellular component: Mitochondrial ATP synthase dimer from Rattus norvegicus
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 13.5 Å
AuthorsChesnokov YM / Kamyshinsky RA
CitationJournal: Nanotechnol Russia / Year: 2020
Title: Determining the Structure and Location of the ATP Synthase in the Membranes of Rat's Heart Mitochondria Using Cryoelectron Tomography
Authors: Nesterov SV / Chesnokov YM / Kamyshinsky RA / Yaguzhinsky LS / Vasilov RG
History
DepositionMay 4, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10998.png

Downloads & links

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Map

FileDownload / File: emd_10998.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 80 pix.
= 296. Å		3.7 Å/pix.
x 80 pix.
= 296. Å		3.7 Å/pix.
x 80 pix.
= 296. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-3.1381617 - 4.5206017
Average (Standard dev.)0.027339332 (±0.60411996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin111
Dimensions808080
Spacing808080
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.73.73.7
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z296.000296.000296.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS111
NC/NR/NS808080
D min/max/mean-3.1384.5210.027

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Supplemental data

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Mask #1

Fileemd_10998_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10998_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10998_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial ATP synthase dimer from Rattus norvegicus

EntireName: Mitochondrial ATP synthase dimer from Rattus norvegicus
Components
  • Organelle or cellular component: Mitochondrial ATP synthase dimer from Rattus norvegicus

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Supramolecule #1: Mitochondrial ATP synthase dimer from Rattus norvegicus

SupramoleculeName: Mitochondrial ATP synthase dimer from Rattus norvegicus
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Wistar rats / Organ: heart / Organelle: Mitochondrion
Molecular weightTheoretical: 600 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2.5 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Cs image corrector (CEOS, Germany)
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average exposure time: 1.5 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 37837 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 18000
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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number subtomograms used: 2768
ExtractionNumber tomograms: 3 / Number images used: 2768 / Software - Name: RELION (ver. 2.1) / Software - details: extraction
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Details: 3D models for the contrast transfer function (CTF) in RELION
Final 3D classificationNumber classes: 1 / Avg.num./class: 2768 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5are

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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