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- EMDB-14135: Bovine complex I in lipid nanodisc, Deactive-ligand (consensus) -

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Basic information

Entry
Database: EMDB / ID: EMD-14135
TitleBovine complex I in lipid nanodisc, Deactive-ligand (consensus)
Map dataLocally sharpened consensus map generated using Phenix Autosharpen
Sample
  • Complex: Consensus map of mitochondrial complex I in the deactive state with a ligand bound
KeywordsMitochondrial complex I / Respiratory complex I / NADH:ubiquinone oxidoreductase / Nanodisc / ELECTRON TRANSPORT
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsChung I / Bridges HR / Hirst J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy
Authors: Chung I / Wright JJ / Bridges HR / Ivanov BS / Biner O / Pereira CS / Arantes GM / Hirst J
History
DepositionJan 13, 2022-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14135.png

Downloads & links

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Map

FileDownload / File: emd_14135.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened consensus map generated using Phenix Autosharpen
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.75 Å/pix.
x 640 pix.
= 479.744 Å		0.75 Å/pix.
x 640 pix.
= 479.744 Å		0.75 Å/pix.
x 640 pix.
= 479.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7496 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.2
Minimum - Maximum-22.166204 - 36.530265999999997
Average (Standard dev.)0.000051981297 (±0.79403454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 479.744 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14135_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Globally sharpened consensus map generated using RELION Postprocess

Fileemd_14135_additional_1.map
AnnotationGlobally sharpened consensus map generated using RELION Postprocess
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 generated using RELION Postprocess (unsharpened...

Fileemd_14135_half_map_1.map
AnnotationHalf map 1 generated using RELION Postprocess (unsharpened and unfiltered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 generated using RELION Postprocess (unsharpened...

Fileemd_14135_half_map_2.map
AnnotationHalf map 2 generated using RELION Postprocess (unsharpened and unfiltered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Consensus map of mitochondrial complex I in the deactive state wi...

EntireName: Consensus map of mitochondrial complex I in the deactive state with a ligand bound
Components
  • Complex: Consensus map of mitochondrial complex I in the deactive state with a ligand bound

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Supramolecule #1: Consensus map of mitochondrial complex I in the deactive state wi...

SupramoleculeName: Consensus map of mitochondrial complex I in the deactive state with a ligand bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#45
Source (natural)Organism: Bos taurus (domestic cattle) / Tissue: Heart / Organelle: Mitochondria
Molecular weightTheoretical: 1 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.78 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMMOPS3-(N-morpholino)propanesulfonic acid
50.0 mMKClpotassium chloride
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ...Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ethanol and dried prior to blotting
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 10 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 6780 / Average exposure time: 2.4 sec. / Average electron dose: 40.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 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

Particle selectionNumber selected: 1078933
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 235957
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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