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- EMDB-28581: Structure of mitochondrial complex I from Drosophila melanogaster... -

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Basic information

Entry
Database: EMDB / ID: EMD-28581
TitleStructure of mitochondrial complex I from Drosophila melanogaster, Flexible-class 1
Map data
Sample
  • Complex: mitochondrial complex I from the thoracic muscles of D. melanogasterRespiratory complex I
    • Protein or peptide: x 42 types
  • Ligand: x 10 types
Function / homology
Function and homology information


Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / NADH dehydrogenase / regulation of terminal button organization / Neutrophil degranulation / ubiquinone-6 biosynthetic process / protein lipoylation ...Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / NADH dehydrogenase / regulation of terminal button organization / Neutrophil degranulation / ubiquinone-6 biosynthetic process / protein lipoylation / cellular respiration / mitochondrial ATP synthesis coupled electron transport / acyl binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / determination of adult lifespan / respirasome / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / response to reactive oxygen species / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / mitochondrial intermembrane space / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / mitochondrion / membrane / metal ion binding / cytoplasm
Similarity search - Function
Complex1_LYR-like / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit ...Complex1_LYR-like / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / Soluble ligand binding domain / SLBB domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NDUFA6, LYR domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NDUFB9, LYR domain / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NAD-dependent epimerase/dehydratase / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH dehydrogenase, subunit C / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-quinone oxidoreductase, chain 5-like / CHCH / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / CHCH domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NAD dependent epimerase/dehydratase family / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial ...NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / GEO11417p1 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Acyl carrier protein, mitochondrial / NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-49kD / NADH dehydrogenase (ubiquinone) 23 kDa subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase (Ubiquinone) 13 kDa B subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A / LD31474p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / RH45008p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / fruit fly (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPadavannil A / Letts JA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137929 United States
CitationJournal: Elife / Year: 2023
Title: Resting mitochondrial complex I from adopts a helix-locked state.
Authors: Abhilash Padavannil / Anjaneyulu Murari / Shauna-Kay Rhooms / Edward Owusu-Ansah / James A Letts /
Abstract: Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the ...Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway 'deactive' state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome . We show that although complex I (-CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of -CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the -CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the -CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover.
History
DepositionOct 15, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_28581.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 512 pix.
= 450.56 Å
0.88 Å/pix.
x 512 pix.
= 450.56 Å
0.88 Å/pix.
x 512 pix.
= 450.56 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.0644338 - 6.016722
Average (Standard dev.)0.0013250788 (±0.094477884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28581_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_28581_half_map_2.map
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Sample components

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Entire : mitochondrial complex I from the thoracic muscles of D. melanogaster

EntireName: mitochondrial complex I from the thoracic muscles of D. melanogasterRespiratory complex I
Components
  • Complex: mitochondrial complex I from the thoracic muscles of D. melanogasterRespiratory complex I
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
    • Protein or peptide: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
    • Protein or peptide: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A
    • Protein or peptide: LD31474p
    • Protein or peptide: NADH dehydrogenase (ubiquinone) 23 kDa subunit
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 3
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 5
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
    • Protein or peptide: Acyl carrier protein, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 subunit C2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
    • Protein or peptide: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A
    • Protein or peptide: GEO11417p1
    • Protein or peptide: Complex I-49kD
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 3
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 2
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4L
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 6
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
    • Protein or peptide: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit
    • Protein or peptide: RH45008p
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
  • Ligand: CARDIOLIPIN
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: mitochondrial complex I from the thoracic muscles of D. melanogaster

SupramoleculeName: mitochondrial complex I from the thoracic muscles of D. melanogaster
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#42
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 16.848254 KDa
SequenceString:

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Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 14.383414 KDa
SequenceString:

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Macromolecule #3: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

MacromoleculeName: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 78.72425 KDa
SequenceString:

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Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 30.013244 KDa
SequenceString:

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Macromolecule #5: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A

MacromoleculeName: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 26.814693 KDa
SequenceString:

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Macromolecule #6: LD31474p

MacromoleculeName: LD31474p / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 24.622855 KDa
SequenceString:

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Macromolecule #7: NADH dehydrogenase (ubiquinone) 23 kDa subunit

MacromoleculeName: NADH dehydrogenase (ubiquinone) 23 kDa subunit / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 24.60998 KDa
SequenceString:

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Macromolecule #8: NADH-ubiquinone oxidoreductase chain 3

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 13.572529 KDa
SequenceString:

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Macromolecule #9: NADH-ubiquinone oxidoreductase chain 1

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 36.38352 KDa
SequenceString:

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Macromolecule #10: NADH-ubiquinone oxidoreductase chain 4

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 51.383047 KDa
SequenceString:

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Macromolecule #11: NADH-ubiquinone oxidoreductase chain 5

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 65.777867 KDa
SequenceString:

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Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 19.87342 KDa
SequenceString:

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Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 14.878194 KDa
SequenceString:

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Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 17.773566 KDa
SequenceString:

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Macromolecule #15: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 12.015969 KDa
SequenceString:

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Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 18.433131 KDa
SequenceString:

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Macromolecule #17: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 18.946418 KDa
SequenceString:

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Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 19.025879 KDa
SequenceString:

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Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 13.157016 KDa
SequenceString:

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Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 13.905104 KDa
SequenceString:

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Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 22.065145 KDa
SequenceString:

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Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 17.416799 KDa
SequenceString:

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Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 16.988021 KDa
SequenceString:

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Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 20.229873 KDa
SequenceString:

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Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 12.113603 KDa
SequenceString:

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Macromolecule #26: Acyl carrier protein, mitochondrial

MacromoleculeName: Acyl carrier protein, mitochondrial / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 17.257992 KDa
SequenceString:

+
Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 subunit C2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 12.925802 KDa
SequenceString:

+
Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 6.232307 KDa
SequenceString:

+
Macromolecule #29: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 20.710354 KDa
SequenceString:

+
Macromolecule #30: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A

MacromoleculeName: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A
type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 46.891699 KDa
SequenceString:

+
Macromolecule #31: GEO11417p1

MacromoleculeName: GEO11417p1 / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 10.758288 KDa
SequenceString:

+
Macromolecule #32: Complex I-49kD

MacromoleculeName: Complex I-49kD / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 52.985953 KDa
SequenceString:

+
Macromolecule #33: NADH dehydrogenase [ubiquinone] flavoprotein 3

MacromoleculeName: NADH dehydrogenase [ubiquinone] flavoprotein 3 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 2.315846 KDa
SequenceString:

+
Macromolecule #34: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 51.898652 KDa
SequenceString:

+
Macromolecule #35: NADH-ubiquinone oxidoreductase chain 2

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 2 / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 39.839887 KDa
SequenceString:

+
Macromolecule #36: NADH-ubiquinone oxidoreductase chain 4L

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4L / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 11.363853 KDa
SequenceString:

+
Macromolecule #37: NADH-ubiquinone oxidoreductase chain 6

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 6 / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 20.083594 KDa
SequenceString:

+
Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 11.562093 KDa
SequenceString:

+
Macromolecule #39: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit

MacromoleculeName: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 13.808102 KDa
SequenceString:

+
Macromolecule #40: RH45008p

MacromoleculeName: RH45008p / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 8.412455 KDa
SequenceString:

+
Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 14.921432 KDa
SequenceString:

+
Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 46.955477 KDa
SequenceString:

+
Macromolecule #43: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 43 / Number of copies: 8 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #44: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 44 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #45: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 45 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

+
Macromolecule #46: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 46 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

+
Macromolecule #47: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 47 / Number of copies: 14 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

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

+
Macromolecule #48: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 48 / Number of copies: 13 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

+
Macromolecule #49: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
type: ligand / ID: 49 / Number of copies: 2 / Formula: ZMP
Molecular weightTheoretical: 568.704 Da
Chemical component information

ChemComp-ZMP:
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate

+
Macromolecule #50: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 50 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

+
Macromolecule #51: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 51 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

+
Macromolecule #52: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 52 / Number of copies: 1 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 293389
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-8esw:
Structure of mitochondrial complex I from Drosophila melanogaster, Flexible-class 1

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