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- EMDB-53469: Membrane domain of Complex I from Ovis aries in presence of D1 in... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-53469
TitleMembrane domain of Complex I from Ovis aries in presence of D1 inhibitor, Open state
Map dataMembrane domain postprocessed focus refined map
Sample
  • Complex: Membrane domain of Complex I from Ovis aries in presence of D1 inhibitor, Open state
KeywordsComplex I / inhibitor / respiration / proton pump / NADH:ubiquinone oxidoreductase / membrane protein / mitochondria / OXIDOREDUCTASE
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSazanov L / Petrova O
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)2RF1AG055549-02A1 United States
CitationJournal: To Be Published
Title: Complex I from Ovis aries in presence of D1 inhibitor
Authors: Sazanov L / Petrova O
History
DepositionApr 22, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53469.png

Downloads & links

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Map

FileDownload / File: emd_53469.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMembrane domain postprocessed focus refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 504 pix.
= 614.88 Å		1.22 Å/pix.
x 504 pix.
= 614.88 Å		1.22 Å/pix.
x 504 pix.
= 614.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.17849128 - 0.508818
Average (Standard dev.)0.00007416922 (±0.014857478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions504504504
Spacing504504504
CellA=B=C: 614.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Membrane domain focus refined map

Fileemd_53469_additional_1.map
AnnotationMembrane domain focus refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_53469_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_53469_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane domain of Complex I from Ovis aries in presence of D1 in...

EntireName: Membrane domain of Complex I from Ovis aries in presence of D1 inhibitor, Open state
Components
  • Complex: Membrane domain of Complex I from Ovis aries in presence of D1 inhibitor, Open state

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Supramolecule #1: Membrane domain of Complex I from Ovis aries in presence of D1 in...

SupramoleculeName: Membrane domain of Complex I from Ovis aries in presence of D1 inhibitor, Open state
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Ovis aries (sheep)
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

Concentration3 mg/mL
BufferpH: 7.4 / Component - Concentration: 20.0 mM / Component - Name: Hepes
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 4167 / Average exposure time: 3.3 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6zki

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76863
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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