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- EMDB-19976: Respiratory complex I from Paracoccus denitrificans in DDM -

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Basic information

Entry
Database: EMDB / ID: EMD-19976
TitleRespiratory complex I from Paracoccus denitrificans in DDM
Map data
Sample
  • Complex: Respiratory complex I
KeywordsRespiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs / OXIDOREDUCTASE
Biological speciesParacoccus denitrificans PD1222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsIvanov BS / Bridges HR / 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: Nat Commun / Year: 2024
Title: Structure of the turnover-ready state of an ancestral respiratory complex I.
Authors: Bozhidar S Ivanov / Hannah R Bridges / Owen D Jarman / Judy Hirst /
Abstract: Respiratory complex I is pivotal for cellular energy conversion, harnessing energy from NADH:ubiquinone oxidoreduction to drive protons across energy-transducing membranes for ATP synthesis. Despite ...Respiratory complex I is pivotal for cellular energy conversion, harnessing energy from NADH:ubiquinone oxidoreduction to drive protons across energy-transducing membranes for ATP synthesis. Despite detailed structural information on complex I, its mechanism of catalysis remains elusive due to lack of accompanying functional data for comprehensive structure-function analyses. Here, we present the 2.3-Å resolution structure of complex I from the α-proteobacterium Paracoccus denitrificans, a close relative of the mitochondrial progenitor, in phospholipid-bilayer nanodiscs. Three eukaryotic-type supernumerary subunits (NDUFS4, NDUFS6 and NDUFA12) plus a novel L-isoaspartyl-O-methyltransferase are bound to the core complex. Importantly, the enzyme is in a single, homogeneous resting state that matches the closed, turnover-ready (active) state of mammalian complex I. Our structure reveals the elements that stabilise the closed state and completes P. denitrificans complex I as a unified platform for combining structure, function and genetics in mechanistic studies.
History
DepositionMar 27, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19976.png

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Map

FileDownload / File: emd_19976.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 450 pix.
= 472.5 Å		1.05 Å/pix.
x 450 pix.
= 472.5 Å		1.05 Å/pix.
x 450 pix.
= 472.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.4044354 - 7.1985874
Average (Standard dev.)0.0016475547 (±0.13836731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 472.49997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19976_msk_1.map
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Half map: #1

Fileemd_19976_half_map_1.map
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Half map: #2

Fileemd_19976_half_map_2.map
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Sample components

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Entire : Respiratory complex I

EntireName: Respiratory complex I
Components
  • Complex: Respiratory complex I

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Supramolecule #1: Respiratory complex I

SupramoleculeName: Respiratory complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

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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

Concentration2.0 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 2278 / Average exposure time: 4.8 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 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: 2.9 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 31572
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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