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- PDB-8qc1: Respiratory complex I from Paracoccus denitrificans in MSP2N2 nan... -

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Basic information

Entry
Database: PDB / ID: 8qc1
TitleRespiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)
Components(NADH dehydrogenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Respiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs
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
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / Chem-P5S / NADH dehydrogenase subunit M / NADH dehydrogenase subunit L
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsIvanov, B.S. / Bridges, H.R. / Hirst, J.
Funding support United Kingdom, 2items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: NADH dehydrogenase subunit M
L: NADH dehydrogenase subunit L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,26017
Polymers134,3312
Non-polymers10,92815
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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NADH dehydrogenase subunit ... , 2 types, 2 molecules ML

#1: Protein NADH dehydrogenase subunit M


Mass: 56519.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B480, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH dehydrogenase subunit L


Mass: 77811.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B481, NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 6 types, 130 molecules

#3: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C39H77O8P
#4: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO10P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Buffer solutionpH: 6.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.4 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 16814
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2EPU2.7image acquisition
4CTFFIND4CTF correction
9PHENIX1.2model refinement
11RELION3.1.0final Euler assignment
12RELION3.1.0classification
13RELION3.1.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146603 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Model Angelo / Source name: Other / Type: in silico model

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