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- EMDB-55034: Reduced bovine complex I in lipid nanodisc, NADH-slack -

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Basic information

Entry
Database: EMDB / ID: EMD-55034
TitleReduced bovine complex I in lipid nanodisc, NADH-slack
Map dataLocally sharpened consensus map generated using Phenix Autosharpen
Sample
  • Complex: Mitochondrial respiratory complex I
KeywordsMitochondrial complex I / Respiratory complex I / NADH:ubiquinone oxidoreductase / Ubiquinone / Nanodisc / NADH / ELECTRON TRANSPORT
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsChung I / Hirst J
Funding support United Kingdom, 3 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
Diamond Light SourceBI22238-37 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Post-catalysis structures of mitochondrial complex I with ubiquinol-10 bound in the active site.
Authors: Injae Chung / Caroline S Pereira / John J Wright / Guilherme M Arantes / Judy Hirst /
Abstract: Respiratory complex I is a multi-subunit energy-transducing membrane enzyme essential for mitochondrial and cellular energy metabolism. It couples NADH oxidation and ubiquinone-10 (Q) reduction to ...Respiratory complex I is a multi-subunit energy-transducing membrane enzyme essential for mitochondrial and cellular energy metabolism. It couples NADH oxidation and ubiquinone-10 (Q) reduction to the concomitant pumping of four protons to generate the proton-motive force that powers oxidative phosphorylation. Despite recent advances in structural knowledge of complex I, many mechanistic aspects including the reactive binding poses of Q, how Q reduction initiates the proton transfer cascade, and how protons move through the membrane domain, remain unclear. Here, we use electron cryomicroscopy to determine structures of mammalian complex I, reconstituted into phospholipid nanodiscs containing exogenous Q and reduced by NADH, to global resolutions of 2.0 to 2.6 Å. Two conformations of a reduced QH molecule are observed, fully inserted into the Q-binding channel in the turnover-relevant closed state. By comparing the quinone species bound in oxidised and reduced complex I structures, paired with molecular dynamics simulations to investigate the charge states of key surrounding residues, we propose a series of substrate binding poses that Q transits through for reduction. Our highly hydrated structures exhibit near-continuous proton-transfer connections along the length of the membrane domain, enabling comparisons between them to assist in identifying the proton-transfer control points that are essential to catalysis.
History
DepositionSep 8, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55034.png

Downloads & links

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Map

FileDownload / File: emd_55034.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.
= 482.4 Å		0.75 Å/pix.
x 640 pix.
= 482.4 Å		0.75 Å/pix.
x 640 pix.
= 482.4 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-15.541048 - 39.129246000000002
Average (Standard dev.)-0.00030135916 (±0.8848004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 482.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55034_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Globally sharpened consensus map generated using RELION Postprocess

Fileemd_55034_additional_1.map
AnnotationGlobally sharpened consensus map generated using RELION Postprocess
Projections & Slices
AxesZYX

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Histogram

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Additional map: Consensus fullmap generated using RELION Refine3D (unsharpened and...

Fileemd_55034_additional_2.map
AnnotationConsensus fullmap generated using RELION Refine3D (unsharpened and unfiltered)
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 generated using RELION Refine3D (unsharpened...

Fileemd_55034_half_map_1.map
AnnotationHalf map 2 generated using RELION Refine3D (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 Refine3D (unsharpened...

Fileemd_55034_half_map_2.map
AnnotationHalf map 1 generated using RELION Refine3D (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 : 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 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: 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

Concentration5.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC7H15NO4SMOPS [3-(N-morpholino)propanesulfonic acid]
50.0 mMKClPotassium chloride
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 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: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Mix with NADH, then blot for 10 seconds before plunging.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
DetailsAutoStigmate and AutoComa on EPU, no AutoCTF
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 13056 / Average exposure time: 2.14 sec. / Average electron dose: 40.29 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: 2.3000000000000003 µm / Nominal defocus min: 0.9 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: 2721931
CTF correctionSoftware: (Name: RELION (ver. 3.1.0), CTFFIND (ver. 4.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

14127

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 75970
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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