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- EMDB-18325: Respiratory complex I from Paracoccus denitrificans in MSP2N2 nan... -

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Basic information

Entry
Database: EMDB / ID: EMD-18325
TitleRespiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)
Map datasharpened map
Sample
  • Complex: Respiratory complex I
    • Protein or peptide: NADH dehydrogenase subunit M
    • Protein or peptide: NADH dehydrogenase subunit L
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CARDIOLIPIN
  • Ligand: CALCIUM ION
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: water
KeywordsRespiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs / OXIDOREDUCTASE
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / endomembrane system / membrane
Similarity search - Function
NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM
Similarity search - Domain/homology
NADH dehydrogenase subunit M / NADH dehydrogenase subunit L
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 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
DepositionAug 25, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18325.png

Downloads & links

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Map

FileDownload / File: emd_18325.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 640 pix.
= 476.8 Å		0.75 Å/pix.
x 640 pix.
= 476.8 Å		0.75 Å/pix.
x 640 pix.
= 476.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.745 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0212
Minimum - Maximum-0.03309542 - 0.0728054
Average (Standard dev.)-0.00022117334 (±0.0018728299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 476.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18325_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_18325_half_map_1.map
Annotationhalf-map 1
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_18325_half_map_2.map
Annotationhalf-map 2
Projections & Slices
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Sample components

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Entire : Respiratory complex I

EntireName: Respiratory complex I
Components
  • Complex: Respiratory complex I
    • Protein or peptide: NADH dehydrogenase subunit M
    • Protein or peptide: NADH dehydrogenase subunit L
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CARDIOLIPIN
  • Ligand: CALCIUM ION
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: water

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Supramolecule #1: Respiratory complex I

SupramoleculeName: Respiratory complex I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)

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Macromolecule #1: NADH dehydrogenase subunit M

MacromoleculeName: NADH dehydrogenase subunit M / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 56.519906 KDa
SequenceString: MTNLLSIITF LPIVAAIIMA LFLRGQDEAA ARNAKWLALL TTTATFVISL FVLFRFDPAN TGFQFVEDHA WIMGLRYKMG VDGISVLFV LLTTFMMPLT ILSTWQVQDK VKEYMIAFLV LEGLMIGVFT ALDLVLFYLF FEAGLIPMFL IIGIWGGKDR I YASFKFFL ...String:
MTNLLSIITF LPIVAAIIMA LFLRGQDEAA ARNAKWLALL TTTATFVISL FVLFRFDPAN TGFQFVEDHA WIMGLRYKMG VDGISVLFV LLTTFMMPLT ILSTWQVQDK VKEYMIAFLV LEGLMIGVFT ALDLVLFYLF FEAGLIPMFL IIGIWGGKDR I YASFKFFL YTFLGSVLML VAMIAMYRMA GTTDIPTLLT FDFPSENFRL LGMTVVGGMQ MLLFLAFFAS FAVKMPMWPV HT WLPDAHV QAPTAGSVLL AAVLLKMGGY GFLRFSLPMF PVASGVAQPY VFWLSAIAIV YTSLVALAQS DMKKVIAYSS VAH MGYVTM GVFAANQIGV DGAIFQMLSH GFISGALFLC VGVIYDRMHT REIDAYGGLV NRMPAYAAVF MFFTMANVGL PGTS GFVGE FLTLMGVFRV DTWVALVATS GVILSAAYAL WLYRRVTLGQ LIKESLKSIT DMTPRERWVF IPLIAMTLIL GVYPR LVTD VTGPAVAALV QDYNQSQPAA PVATAQASH

UniProtKB: NADH dehydrogenase subunit M

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Macromolecule #2: NADH dehydrogenase subunit L

MacromoleculeName: NADH dehydrogenase subunit L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 77.811352 KDa
SequenceString: MEKFVLFAPL IASLIAGLGW RAIGEKAAQY LTTGVLFLSC LISWYLFLSF DGVPRHIPVL DWVVTGDFHA EWAIRLDRLT AIMLIVVTT VSALVHMYSL GYMAHDDNWT HDEHYKARFF AYLSFFTFAM LMLVTADNLL QMFFGWEGVG VASYLLIGFY Y KKASANAA ...String:
MEKFVLFAPL IASLIAGLGW RAIGEKAAQY LTTGVLFLSC LISWYLFLSF DGVPRHIPVL DWVVTGDFHA EWAIRLDRLT AIMLIVVTT VSALVHMYSL GYMAHDDNWT HDEHYKARFF AYLSFFTFAM LMLVTADNLL QMFFGWEGVG VASYLLIGFY Y KKASANAA AMKAFIVNRV GDFGFLLGIF GIYWLTGSVQ FDEIFRQVPQ LAQTEMHFLW RDWNAANLLG FLLFVGAMGK SA QLLLHTW LPDAMEGPTP VSALIHAATM VTAGVFLVCR MSPLYEFAPD AKNFIVIIGA TTAFFAATVG LVQNDIKRVI AYS TCSQLG YMFVAAGVGV YSAAMFHLLT HAFFKAMLFL GAGSVIHAMH HEQDMRNYGG LRKKIPLTFW AMMIGTFAIT GVGI PLTHL GFAGFLSKDA IIESAYAGSG YAFWLLVIAA CFTSFYSWRL IFLTFYGKPR GDHHAHDHAH ESPPVMTIPL GVLAI GAVF AGMVWYGPFF GDHHKVTEYF HIAGAHHEAA EGEEAEHATA EAPVEHAVAD TATAEGEAAA EAEHAEIAAP VGGAIY MHP DNHIMDEAHH APAWVKVSPF VAMVLGLITA WTFYIANPSL PRRLAAQQPA LYRFLLNKWY FDEIYEFIFV RPAKWLG RV LWKGGDGAVI DGTINGVAMG LIPRLTRAAV RVQSGYLFHY AFAMVLGIVG LLIWVMMRGA H

UniProtKB: NADH dehydrogenase subunit L

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Macromolecule #3: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 4 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #5: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 5 / Number of copies: 1 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phospho...

MacromoleculeName: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
type: ligand / ID: 7 / Number of copies: 1 / Formula: P5S
Molecular weightTheoretical: 792.075 Da
Chemical component information

ChemComp-P5S:
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 115 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 16814 / Average exposure time: 2.4 sec. / Average electron dose: 40.0 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: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 146603
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

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Model Angelo
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8qc1:
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)

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