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- EMDB-18324: Respiratory complex I from Paracoccus denitrificans in MSP2N2 nan... -

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Basic information

Entry
Database: EMDB / ID: EMD-18324
TitleRespiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs
Map dataGlobally sharpened consensus map
Sample
  • Complex: Respiratory complex I
    • Protein or peptide: x 18 types
  • Ligand: x 13 types
KeywordsRespiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs / OXIDOREDUCTASE
Function / homology
Function and homology information


protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / NADH:ubiquinone reductase (H+-translocating) / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase activity ...protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / NADH:ubiquinone reductase (H+-translocating) / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / endomembrane system / aerobic respiration / electron transport chain / protein modification process / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / methylation / response to oxidative stress / iron ion binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial ...Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / SLBB domain / : / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / : / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
NADH:ubiquinone oxidoreductase 17.2 kD subunit / ETC complex I subunit conserved region / Zinc finger CHCC-type domain-containing protein / NADH-quinone oxidoreductase subunit N / NADH dehydrogenase subunit M / NADH dehydrogenase subunit L / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase ...NADH:ubiquinone oxidoreductase 17.2 kD subunit / ETC complex I subunit conserved region / Zinc finger CHCC-type domain-containing protein / NADH-quinone oxidoreductase subunit N / NADH dehydrogenase subunit M / NADH dehydrogenase subunit L / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH dehydrogenase subunit E / NADH-quinone oxidoreductase subunit D / NADH-quinone oxidoreductase subunit C / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit A / Protein-L-isoaspartate O-methyltransferase / NADH-quinone oxidoreductase chain 10
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 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_18324.png

Downloads & links

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Map

FileDownload / File: emd_18324.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobally sharpened consensus 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: 0.019
Minimum - Maximum-0.043334004 - 0.11134344
Average (Standard dev.)-0.00014545044 (±0.002713615)
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_18324_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_18324_half_map_1.map
AnnotationHalf-map 2
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

Fileemd_18324_half_map_2.map
AnnotationHalf-map 1
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 : Respiratory complex I

EntireName: Respiratory complex I
Components
  • Complex: Respiratory complex I
    • Protein or peptide: NADH-quinone oxidoreductase subunit K
    • Protein or peptide: NADH-quinone oxidoreductase
    • Protein or peptide: Protein-L-isoaspartate O-methyltransferase
    • Protein or peptide: NADH-quinone oxidoreductase subunit I
    • Protein or peptide: NADH dehydrogenase subunit E
    • Protein or peptide: NADH-quinone oxidoreductase subunit N
    • Protein or peptide: NADH-quinone oxidoreductase subunit H
    • Protein or peptide: NADH-quinone oxidoreductase subunit F
    • Protein or peptide: NADH-quinone oxidoreductase subunit D
    • Protein or peptide: NADH:ubiquinone oxidoreductase 17.2 kD subunit
    • Protein or peptide: NADH-quinone oxidoreductase subunit A
    • Protein or peptide: NADH-quinone oxidoreductase chain 10
    • Protein or peptide: Zinc finger CHCC-type domain-containing protein
    • Protein or peptide: ETC complex I subunit conserved region
    • Protein or peptide: NADH-quinone oxidoreductase subunit C
    • Protein or peptide: NADH-quinone oxidoreductase subunit B
    • Protein or peptide: NADH dehydrogenase subunit L
    • Protein or peptide: NADH dehydrogenase subunit M
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: SODIUM ION
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
  • Ligand: CALCIUM ION
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: CARDIOLIPIN
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: ZINC ION
  • Ligand: UBIQUINONE-10
  • Ligand: water

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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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Macromolecule #1: NADH-quinone oxidoreductase subunit K

MacromoleculeName: NADH-quinone oxidoreductase subunit K / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 10.863054 KDa
SequenceString:
MIGLTHYLVV GAILFVTGIF GIFVNRKNVI VILMSIELML LAVNINFVAF STHLGDLAGQ VFTMFVLTVA AAEAAIGLAI LVVFFRNRG TIAVEDVNVM KG

UniProtKB: NADH-quinone oxidoreductase subunit K

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Macromolecule #2: NADH-quinone oxidoreductase

MacromoleculeName: NADH-quinone oxidoreductase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 73.289398 KDa
SequenceString: MADLRKIKID DTIIEVDPNM TLIQACEMAG IEVPRFCYHE RLSIAGNCRM CLVEVVGGPP KPAASCAMQV KDLRPGPEGA PSEIRTNSP MVKKAREGVM EFLLINHPLD CPICDQGGEC DLQDQAMAYG VDFSRYREPK RATEDLNLGP LVETHMTRCI S CTRCVRFT ...String:
MADLRKIKID DTIIEVDPNM TLIQACEMAG IEVPRFCYHE RLSIAGNCRM CLVEVVGGPP KPAASCAMQV KDLRPGPEGA PSEIRTNSP MVKKAREGVM EFLLINHPLD CPICDQGGEC DLQDQAMAYG VDFSRYREPK RATEDLNLGP LVETHMTRCI S CTRCVRFT TEVAGITQMG QTGRGEDSEI TSYLNQTLES NMQGNIIDLC PVGALVSKPY AFTARPWELT KTESIDVMDA LG SSIRIDT KGREVMRILP RNHDGVNEEW ISDKTRFVWD GLRRQRLDRP YIRENGRLRP ASWPEALEAA ARAMKGKKIA GLI GDLVPA EAAFSLKQLV EGLGGKVECR VDGARLPAGN RSAYVGTARI EDIDDAEMIQ LIGTNPRDEA PVLNARIRKA WSKG AKVGL VGEPVDLTYD YAHVGTDRAA LESLSSREIS DETKARPSIV IVGQGAIREA DGEAVLAHAM KLAENSNSGL LILHT AAGR VGAMDVGAVT EGGLLAAIDG AEVVYNLGAD EVDIDQGPFV IYQGSHGDRG AHRADIILPG ACYTEESGLF VNTEGR PQL AMRANFAPGE GKENWAILRA LSAELGATQP WDSLAGLRRK LVEAVPHLAQ IDQVPQNEWQ PLGRFDLGQA SFRYAIR DF YLTNPIARSS PLMGELSAMA AARKAPAPLA AE

UniProtKB: NADH-quinone oxidoreductase

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Macromolecule #3: Protein-L-isoaspartate O-methyltransferase

MacromoleculeName: Protein-L-isoaspartate O-methyltransferase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 23.528947 KDa
SequenceString: MTDFAQRRTM MVDTQVRPNE VTSYPVIEAM LNVPREQFVP ESRRDVAYVG NNIDLAPGRV LLEPRTLGKM MDILNLQNGD LVLDVGCGY GYSAAVMARI AEAVVAVEED AAMAAEAEGR LAAQDVFNVA VVQGALAEGC PGQAPYDAIL IEGAVEQVPE A LTEQLREG ...String:
MTDFAQRRTM MVDTQVRPNE VTSYPVIEAM LNVPREQFVP ESRRDVAYVG NNIDLAPGRV LLEPRTLGKM MDILNLQNGD LVLDVGCGY GYSAAVMARI AEAVVAVEED AAMAAEAEGR LAAQDVFNVA VVQGALAEGC PGQAPYDAIL IEGAVEQVPE A LTEQLREG GRIVALFREG NLGIVRLGHK LDGRVNWRFA FNAVAPLLPG FARPRGFVL

UniProtKB: Protein-L-isoaspartate O-methyltransferase

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Macromolecule #4: NADH-quinone oxidoreductase subunit I

MacromoleculeName: NADH-quinone oxidoreductase subunit I / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 18.925561 KDa
SequenceString:
MAFDFARATK YFLMWDFIKG FGLGMRYFVS PKPTLNYPHE KGPLSPRFRG EHALRRYPNG EERCIACKLC EAVCPAQAIT IDAEPREDG SRRTTRYDID MTKCIYCGFC QEACPVDAIV EGPNFEYATE TREELFYDKQ KLLANGERWE AEIARNLQLD A PYR

UniProtKB: NADH-quinone oxidoreductase subunit I

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Macromolecule #5: NADH dehydrogenase subunit E

MacromoleculeName: NADH dehydrogenase subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 26.145865 KDa
SequenceString: MLRRLSPIQP DSFEFTPANL EWARAQMTKY PEGRQQSAII PVLWRAQEQE GWLSRPAIEY CADLLGMPYI RALEVATFYF MFQLQPVGS VAHIQICGTT TCMICGAEDL IRVCKEKIAP EPHALSADGR FSWEEVECLG ACTNAPMAQI GKDFYEDLTV E KLAALIDR ...String:
MLRRLSPIQP DSFEFTPANL EWARAQMTKY PEGRQQSAII PVLWRAQEQE GWLSRPAIEY CADLLGMPYI RALEVATFYF MFQLQPVGS VAHIQICGTT TCMICGAEDL IRVCKEKIAP EPHALSADGR FSWEEVECLG ACTNAPMAQI GKDFYEDLTV E KLAALIDR FAAGEVPVPG PQNGRFSAEA LGGPTALADL KGGEAHNASV ARALRLGDSI KRIDGTEVPI TTPWLATQNG V

UniProtKB: NADH dehydrogenase subunit E

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Macromolecule #6: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 52.56482 KDa
SequenceString: MTSLDFSTIL PEVVLAGYAL AALMAGAYLG KDRLARTLLW VTVAAFLVVA AMVGLGNHVD GAAFHGMFID DGFSRFAKVV TLVAAAGVL AMSADYMQRR NMLRFEFPII VALAVLGMMF MVSAGDLLTL YMGLELQSLA LYVVAAMRRD SVRSSEAGLK Y FVLGSLSS ...String:
MTSLDFSTIL PEVVLAGYAL AALMAGAYLG KDRLARTLLW VTVAAFLVVA AMVGLGNHVD GAAFHGMFID DGFSRFAKVV TLVAAAGVL AMSADYMQRR NMLRFEFPII VALAVLGMMF MVSAGDLLTL YMGLELQSLA LYVVAAMRRD SVRSSEAGLK Y FVLGSLSS GLLLYGASLV YGFAGTTGFE GIISTIEAGH LSLGVLFGLV FMLVGLSFKV SAVPFHMWTP DVYEGSPTPV TA FFATAPK VAAMALIARL VFDAFGHVIG DWSQIVAALA VMSMFLGSIA GIGQTNIKRL MAYSSIAHMG FALVGLAAGT AIG VQNMLL YMTIYAVMNI GTFAFILSME RDGVPVTDLA ALNRFAWTDP VKALAMLVLM FSLAGVPPTL GFFAKFGVLT AAVD AGMGW LAVLGVIASV IGAFYYLRIV YYMYFGGESE GMTSRMGAVQ YLALMVPALA MLVGAISMFG VDSAAGRAAE TLVGP VAAI EQPAEAAQAE PVQGE

UniProtKB: NADH-quinone oxidoreductase subunit N

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Macromolecule #7: NADH-quinone oxidoreductase subunit H

MacromoleculeName: NADH-quinone oxidoreductase subunit H / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 38.861152 KDa
SequenceString: MAEFWASPYG FALSMLLQGL AVIAFVMGSL IFMVYGDRKI WAAVQMRRGP NVVGPWGLLQ TFADALKYIV KEIVIPAGAD KFVYFLAPF LSMMLALFAF VVIPFDEGWV MANINVGILF IFAASSLEVY GVIMGGWASN SKYPFLASLR SAAQMISYEV S LGLIIIGI ...String:
MAEFWASPYG FALSMLLQGL AVIAFVMGSL IFMVYGDRKI WAAVQMRRGP NVVGPWGLLQ TFADALKYIV KEIVIPAGAD KFVYFLAPF LSMMLALFAF VVIPFDEGWV MANINVGILF IFAASSLEVY GVIMGGWASN SKYPFLASLR SAAQMISYEV S LGLIIIGI IISTGSMNLT AIVEAQRGDY GLLNWYWLPH LPMVVLFFVS ALAECNRPPF DLVEAESELV AGFMTEYSST PY LLFMAGE YIAMYLMCAL LSLLFFGGWL SPVPFIADGW WWMVIKMWFW FYMFAMVKAI VPRYRYDQLM RIGWKVFLPL SLG WVVLVA ILARYEILGG FWARFAVGG

UniProtKB: NADH-quinone oxidoreductase subunit H

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Macromolecule #8: NADH-quinone oxidoreductase subunit F

MacromoleculeName: NADH-quinone oxidoreductase subunit F / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 47.281141 KDa
SequenceString: MLNDQDRIFT NLYGMGDRSL AGAKKRGHWD GTAAIIQRGR DKIIDEMKAS GLRGRGGAGF PTGMKWSFMP KESDGRPSYL VINADESEP ATCKDREIMR HDPHTLIEGA LIASFAMGAH AAYIYIRGEF IREREALQAA IDECYDAGLL GRNAAGSGWD F DLYLHHGA ...String:
MLNDQDRIFT NLYGMGDRSL AGAKKRGHWD GTAAIIQRGR DKIIDEMKAS GLRGRGGAGF PTGMKWSFMP KESDGRPSYL VINADESEP ATCKDREIMR HDPHTLIEGA LIASFAMGAH AAYIYIRGEF IREREALQAA IDECYDAGLL GRNAAGSGWD F DLYLHHGA GAYICGEETA LLESLEGKKG MPRMKPPFPA GAGLYGCPTT VNNVESIAVV PTILRRGAEW FASFGRPNNA GV KLFGLTG HVNTPCVVEE AMSIPMRELI EKHGGGIRGG WKNLKAVIPG GASCPVLTAE QCENAIMDYD GMRELRSSFG TAC MIVMDQ STDVVKAIWR LSKFFKHESC GQCTPCREGT GWMMRVMERL VRGDAEVEEI DMLFDVTKQV EGHTICALGD AAAW PIQGL IRNFREEIED RIKAKRTGRM GAMAAE

UniProtKB: NADH-quinone oxidoreductase subunit F

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Macromolecule #9: NADH-quinone oxidoreductase subunit D

MacromoleculeName: NADH-quinone oxidoreductase subunit D / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 46.811484 KDa
SequenceString: MDGDIRKNSY DDGSMDALTG EQSIRNFNIN FGPQHPAAHG VLRMVLELDG EIVERADPHI GLLH(2MR)GTEKL MESRTY LQN LPYLDRLDYV APMNQEHAWC LAIERLTGTV IPRRASLIRV LYSEIGRILN HLMGVTTGAM DVGALTPPLW GFEAREE LM IFYERACGAR ...String:
MDGDIRKNSY DDGSMDALTG EQSIRNFNIN FGPQHPAAHG VLRMVLELDG EIVERADPHI GLLH(2MR)GTEKL MESRTY LQN LPYLDRLDYV APMNQEHAWC LAIERLTGTV IPRRASLIRV LYSEIGRILN HLMGVTTGAM DVGALTPPLW GFEAREE LM IFYERACGAR LHAAYFRPGG VHQDLPPDLL DDIEEWCERF PKLVDDLDTL LTENRIFKQR LVDIGIVTEA DALDWGYT G VMVRGSGLAW DLRRSQPYEC YDEFDFQIPV GRNGDCYDRY LCRMAEMRES CKIMQQAVQK LRAEPAGDVL ARGKLTPPR RAEMKRDMES LIHHFKLYTE GFKVPAGEVY AAVEAPKGEF GVYLVADGTN KPWRAKLRAP GFAHLQSIDW MSRGHMLADV PAIIATLDI VFGEVDR

UniProtKB: NADH-quinone oxidoreductase subunit D

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Macromolecule #10: NADH:ubiquinone oxidoreductase 17.2 kD subunit

MacromoleculeName: NADH:ubiquinone oxidoreductase 17.2 kD subunit / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 14.432875 KDa
SequenceString:
MSFLLRFLTW WNSQTLNTQV WTKLYGEKVG EDDQGNVYYQ SGGGKRRWVI YNGESEASRI SPEWHGWLHH TYKEPPTAAP LAHKPWEKP HEPNLTGSSG AYHPAGSLYR AQPVERRDYD AWQPE

UniProtKB: NADH:ubiquinone oxidoreductase 17.2 kD subunit

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Macromolecule #11: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 13.686093 KDa
SequenceString:
(FME)EYLLQEYLP ILVFLGMASA LAIVLILAAA VIAVRNPDPE KVSAYECGFN AFDDARMKFD VRFYLVSILF IIFDLE VAF LFPWAVSFAS LSDVAFWGMM VFLAVLTVGF AYEWKKGALE WA

UniProtKB: NADH-quinone oxidoreductase subunit A

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Macromolecule #12: NADH-quinone oxidoreductase chain 10

MacromoleculeName: NADH-quinone oxidoreductase chain 10 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 21.835205 KDa
SequenceString: MMTFAFYLFA ISACVAGFMV VIGRNPVHSV LWLILAFLSA AGLFVLQGAE FVAMLLVVVY VGAVAVLFLF VVMMLDVDFA ELKGELARY LPLALVIGVV LLAQLGIAFS GWTPSDQAES LRAAPVDAAV ENTLGLGLVL YDRYVLMFQL AGLVLLVAMI G AIVLTMRH ...String:
MMTFAFYLFA ISACVAGFMV VIGRNPVHSV LWLILAFLSA AGLFVLQGAE FVAMLLVVVY VGAVAVLFLF VVMMLDVDFA ELKGELARY LPLALVIGVV LLAQLGIAFS GWTPSDQAES LRAAPVDAAV ENTLGLGLVL YDRYVLMFQL AGLVLLVAMI G AIVLTMRH RKDVKRQNVL EQMWRDPAKT MELKDVKPGQ GL

UniProtKB: NADH-quinone oxidoreductase chain 10

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Macromolecule #13: Zinc finger CHCC-type domain-containing protein

MacromoleculeName: Zinc finger CHCC-type domain-containing protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 7.069931 KDa
SequenceString:
MTIPAPEIQT VTSWKVACDG DEARGLGHPR VWLAIPRDTG WVECGYCDKR FVIDREHAHD DH

UniProtKB: Zinc finger CHCC-type domain-containing protein

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Macromolecule #14: ETC complex I subunit conserved region

MacromoleculeName: ETC complex I subunit conserved region / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 12.048399 KDa
SequenceString:
MRVRIYKPAR NAMQSGTART RNWVLDFPPA DPRAIDPLMG WTSSDDTQSQ VRLRFETRKQ AEDYAREHGL DYEVIEPHTR AANIRPRGY GENFASDRRA PWTH

UniProtKB: ETC complex I subunit conserved region

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Macromolecule #15: NADH-quinone oxidoreductase subunit C

MacromoleculeName: NADH-quinone oxidoreductase subunit C / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 23.920102 KDa
SequenceString: MSEALSDEAL LELAEHIALR RENDVISTQV AFGELTVNAT LSGVIGLIEF LRNDPNCRFS TLIDITAVDN PARPARFDVV YHLLSMYQN QRIRVKVQVR EDELVPSLIG VFPGANWYER EVFDLFGILF SGHSDLRRIL TDYGFRGHPL RKDFPTTGYV E VRWSDIEK ...String:
MSEALSDEAL LELAEHIALR RENDVISTQV AFGELTVNAT LSGVIGLIEF LRNDPNCRFS TLIDITAVDN PARPARFDVV YHLLSMYQN QRIRVKVQVR EDELVPSLIG VFPGANWYER EVFDLFGILF SGHSDLRRIL TDYGFRGHPL RKDFPTTGYV E VRWSDIEK RVVYEPVNLV QEYRQFDFLS PWEGAKYVLP GDEKAPEAKK

UniProtKB: NADH-quinone oxidoreductase subunit C

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Macromolecule #16: NADH-quinone oxidoreductase subunit B

MacromoleculeName: NADH-quinone oxidoreductase subunit B / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 19.525543 KDa
SequenceString:
MMTGLNTAGA DRDLATAELN RELQDKGFLL TTTEDIINWA RNGSLHWMTF GLACCAVEMM QTSMPRYDLE RFGTAPRASP RQSDLMIVA GTLTNKMAPA LRKVYDQMPE PRYVISMGSC ANGGGYYHYS YSVVRGCDRI VPVDIYVPGC PPTAEALLYG I LQLQRRIR RTGTLVR

UniProtKB: NADH-quinone oxidoreductase subunit B

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Macromolecule #17: NADH dehydrogenase subunit L

MacromoleculeName: NADH dehydrogenase subunit L / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
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 #18: NADH dehydrogenase subunit M

MacromoleculeName: NADH dehydrogenase subunit M / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
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 #19: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 19 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #20: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 20 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #21: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 21 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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Macromolecule #22: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 22 / Number of copies: 17 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

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

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Macromolecule #23: 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: 23 / Number of copies: 2 / 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 #24: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 24 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #25: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 25 / Number of copies: 10 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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Macromolecule #26: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 26 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #27: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 27 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

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Macromolecule #28: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 28 / Number of copies: 2 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #29: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 29 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #30: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 30 / Number of copies: 1 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10

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Macromolecule #31: water

MacromoleculeName: water / type: ligand / ID: 31 / Number of copies: 1080 / 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
GridModel: UltrAuFoil R0./1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
Details: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for ...Details: The grids were glow discharged at 20 mA for 90 s to clean and increase the hydrophilicity of the grid surface and then incubated in 5 mM 11-mercaptoundecyl hexaethyleneglycol in ethanol for two days under anaerobic conditions. The grids were then washed in 100% ethanol and dried three times prior to sample application.
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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.3 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-8qby:
Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs

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