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- EMDB-15216: Complex I inhibited by rotenone open3 -

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Basic information

Entry
Database: EMDB / ID: EMD-15216
TitleComplex I inhibited by rotenone open3
Map data
Sample
  • Complex: Complex I inhibited by rotenone, open3
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKampjut D / Sazanov LA
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Commission653706European Union
European Commission665385European Union
CitationJournal: Science / Year: 2020
Title: The coupling mechanism of mammalian respiratory complex I.
Authors: Domen Kampjut / Leonid A Sazanov /
Abstract: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.
History
DepositionJun 20, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15216.png

Downloads & links

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Map

FileDownload / File: emd_15216.map.gz / Format: CCP4 / Size: 29.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 163 pix.
= 172.943 Å		1.06 Å/pix.
x 178 pix.
= 188.858 Å		1.06 Å/pix.
x 270 pix.
= 286.47 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.11864378 - 0.44190264
Average (Standard dev.)0.0031492873 (±0.02777916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions178270163
Spacing163178270
CellA: 172.943 Å / B: 188.858 Å / C: 286.47 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15216_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15216_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 : Complex I inhibited by rotenone, open3

EntireName: Complex I inhibited by rotenone, open3
Components
  • Complex: Complex I inhibited by rotenone, open3

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Supramolecule #1: Complex I inhibited by rotenone, open3

SupramoleculeName: Complex I inhibited by rotenone, open3 / type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Ovis aries (sheep)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5lnk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55837
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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