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- EMDB-15938: Drosophila melanogaster complex I in the Cracked state (Dm3) -

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Basic information

Entry
Database: EMDB / ID: EMD-15938
TitleDrosophila melanogaster complex I in the Cracked state (Dm3)
Map dataGlobally sharpened consensus map generated using RELION Postprocess
Sample
  • Complex: Mitochondrial respiratory complex I
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsAgip AA / Chung I / Sanchez-Martinez A / Whitworth AJ / Hirst J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00028/1 United Kingdom
CitationJournal: Elife / Year: 2023
Title: Cryo-EM structures of mitochondrial respiratory complex I from .
Authors: Ahmed-Noor A Agip / Injae Chung / Alvaro Sanchez-Martinez / Alexander J Whitworth / Judy Hirst /
Abstract: Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a ...Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states, the ubiquinone-binding site is unchanged, but a deactive-type π-bulge is present in ND6-TMH3. Our detailed structural knowledge of complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology.
History
DepositionOct 10, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15938.png

Downloads & links

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Map

FileDownload / File: emd_15938.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobally sharpened consensus map generated using RELION Postprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 450 pix.
= 471.6 Å		1.05 Å/pix.
x 450 pix.
= 471.6 Å		1.05 Å/pix.
x 450 pix.
= 471.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0128604835 - 0.097273454
Average (Standard dev.)-0.00019977044 (±0.0022414636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 471.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15938_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unsharpened and unfiltered consensus map generated using RELION...

Fileemd_15938_additional_1.map
AnnotationUnsharpened and unfiltered consensus map generated using RELION Postprocess
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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

Fileemd_15938_half_map_1.map
AnnotationHalf map 2 generated using RELION Postprocess (unsharpened and unfiltered)
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_15938_half_map_2.map
AnnotationHalf map 1 generated using RELION Postprocess (unsharpened and unfiltered)
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial respiratory complex I

EntireName: Mitochondrial respiratory complex I
Components
  • Complex: Mitochondrial respiratory complex I

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Supramolecule #1: Mitochondrial respiratory complex I

SupramoleculeName: Mitochondrial respiratory complex I / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#43
Details: Native purification of mitochondrial complex I from Drosophila melanogaster (fruit fly) W1118.
Source (natural)Organism: Drosophila melanogaster (fruit fly) / Strain: W1118
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

Concentration3.4 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTRIZMA base
150.0 mMNaClsodium chloride
0.05 %DDMn-Dodecyl beta-D-maltoside
GridModel: UltrAuFoil / 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 7 days 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 7 days 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: 100 % / 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 K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3082 / Average exposure time: 10.0 sec. / Average electron dose: 41.88 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: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
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: 194538
Startup modelType of model: EMDB MAP
EMDB ID:

4345

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 13520
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6zr2

RefinementSpace: REAL

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