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- PDB-9ce2: Respiratory supercomplex I+III2+IV open state -

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Basic information

Entry
Database: PDB / ID: 9ce2
TitleRespiratory supercomplex I+III2+IV open state
Components
  • (Cytochrome b-c1 complex subunit ...) x 6
  • (Cytochrome c oxidase subunit ...) x 12
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 10
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase subunit ...) x 2
  • (Ubiquinol-cytochrome c ...) x 2
  • Acyl carrier protein
  • Cytochrome b
  • Cytochrome c oxidase subunit
  • Cytochrome c1
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsELECTRON TRANSPORT / electron transporter / heart / respiratory supercomplex
Function / homology
Function and homology information


Complex IV assembly / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Complex III assembly / Mitochondrial protein import / respiratory chain complex IV assembly / : / subthalamus development / pons development / mitochondrial respirasome assembly ...Complex IV assembly / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Complex III assembly / Mitochondrial protein import / respiratory chain complex IV assembly / : / subthalamus development / pons development / mitochondrial respirasome assembly / RHOG GTPase cycle / cerebellar Purkinje cell layer development / Complex I biogenesis / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / Neutrophil degranulation / pyramidal neuron development / Mitochondrial protein degradation / respiratory chain complex IV / thalamus development / mesenchymal stem cell proliferation / respiratory chain complex / reproductive system development / cytochrome-c oxidase / mesenchymal stem cell differentiation / circulatory system development / respiratory chain complex III / oxidative phosphorylation / cardiac muscle tissue development / mitochondrial electron transport, cytochrome c to oxygen / oxidoreductase activity, acting on NAD(P)H / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / stem cell division / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / ubiquinone binding / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / regulation of mitochondrial membrane potential / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / central nervous system development / respiratory electron transport chain / hippocampus development / DNA damage response, signal transduction by p53 class mediator / kidney development / fatty acid metabolic process / electron transport chain / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / multicellular organism growth / NAD binding / fatty acid biosynthetic process / cellular senescence / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / gene expression / electron transfer activity / oxidoreductase activity / mitochondrial inner membrane / nuclear body / mitochondrial matrix / copper ion binding / heme binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / membrane
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Globular protein, non-globular alpha/beta subunit / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / : / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Cytochrome b-c1 complex subunit 7 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Cytochrome b-c1 complex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Cytochrome c oxidase subunit / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Cytochrome c oxidase subunit 4 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Cytochrome c oxidase subunit 6C / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Cytochrome b-c1 complex subunit 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Cytochrome b-c1 complex subunit 8 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Cytochrome c oxidase subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / Cytochrome c oxidase subunit 8 / Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 / Cytochrome b-c1 complex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Cytochrome b-c1 complex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / Cytochrome c oxidase subunit 1 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 6 / Cytochrome c oxidase subunit 2 / NADH-ubiquinone oxidoreductase chain 4L / Cytochrome b / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 7A1, mitochondrial / NADH-ubiquinone oxidoreductase chain 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsZhang, Z. / Maharjan, R. / Tringides, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Respiratory supercomplex I+III2+IV open state
Authors: Zhang, Z. / Maharjan, R. / Tringides, M.
History
DepositionJun 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Cytochrome b-c1 complex subunit 6, mitochondrial
1: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
2: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1
3: Cytochrome b-c1 complex subunit 10
4: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1
6: Cytochrome b-c1 complex subunit 2, mitochondrial
7: Cytochrome b
8: Cytochrome c1
9: Cytochrome b-c1 complex subunit 7
A: Cytochrome c oxidase subunit 6C
a: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
b: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
c: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
d: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
e: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
f: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
g: NADH dehydrogenase [ubiquinone] 1 subunit C2
h: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
i: NADH-ubiquinone oxidoreductase chain 2
j: NADH-ubiquinone oxidoreductase chain 3
k: NADH-ubiquinone oxidoreductase chain 4L
m: NADH-ubiquinone oxidoreductase chain 6
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
q: NADH-ubiquinone oxidoreductase chain 4
r: NADH-ubiquinone oxidoreductase chain 1
B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
F: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
H: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
J: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
K: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1
O: Acyl carrier protein
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
R: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
T: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
U: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
W: NADH:ubiquinone oxidoreductase subunit A13
X: Acyl carrier protein
Y: NADH:ubiquinone oxidoreductase subunit B2
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
l: NADH-ubiquinone oxidoreductase chain 5
s: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
t: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
u: Cytochrome b-c1 complex subunit 1, mitochondrial
v: Cytochrome b-c1 complex subunit 2, mitochondrial
w: Cytochrome b
x: Cytochrome c1
y: Cytochrome b-c1 complex subunit 7
z: Cytochrome b-c1 complex subunit 8
Aa: Cytochrome b-c1 complex subunit 8
Ab: Cytochrome b-c1 complex subunit 6, mitochondrial
Ac: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
Ad: Cytochrome b-c1 complex subunit 10
Ag: Cytochrome c oxidase subunit 8
Ah: Cytochrome c oxidase subunit 7A1, mitochondrial
Ai: Cytochrome c oxidase subunit 7B
Aj: Cytochrome c oxidase subunit 7C, mitochondrial
Ak: Cytochrome c oxidase subunit 1
Al: Cytochrome c oxidase subunit 2
Am: Cytochrome c oxidase subunit 3
An: Cytochrome c oxidase subunit 4
Ao: Cytochrome c oxidase subunit 5A, mitochondrial
Ap: Cytochrome c oxidase subunit 5B, mitochondrial
Aq: Cytochrome c oxidase subunit 6A2
Ar: Cytochrome c oxidase subunit
5: Cytochrome b-c1 complex subunit 1, mitochondrial
G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
L: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
M: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
Ae: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1
Af: Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,894,732101
Polymers1,884,73980
Non-polymers9,99221
Water00
1


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

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Components

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Cytochrome b-c1 complex subunit ... , 6 types, 12 molecules 0Ab3Ad6v9yu5zAa

#1: Protein Cytochrome b-c1 complex subunit 6, mitochondrial


Mass: 10685.803 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1JI21
#4: Protein Cytochrome b-c1 complex subunit 10


Mass: 6560.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SDI2
#5: Protein Cytochrome b-c1 complex subunit 2, mitochondrial


Mass: 48262.434 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RPD2
#8: Protein Cytochrome b-c1 complex subunit 7


Mass: 13587.549 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZPR8
#51: Protein Cytochrome b-c1 complex subunit 1, mitochondrial


Mass: 52756.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0PK14
#52: Protein Cytochrome b-c1 complex subunit 8


Mass: 9784.339 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0SHY6

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Ubiquinol-cytochrome c ... , 2 types, 6 molecules 1Ac24AeAf

#2: Protein Ubiquinol-cytochrome c reductase complex 7.2 kDa protein / cytochrome b-c1 complex subunit 9


Mass: 7412.530 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1J3N6
#3: Protein
Ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1


Mass: 32174.654 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNZ1

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Protein , 5 types, 8 molecules 7w8xOXArG

#6: Protein Cytochrome b


Mass: 42840.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1HBG9
#7: Protein Cytochrome c1


Mass: 35488.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AZF9
#37: Protein Acyl carrier protein


Mass: 17308.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1WW27
#64: Protein Cytochrome c oxidase subunit


Mass: 10170.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0W345
#65: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 79627.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ARY3

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Cytochrome c oxidase subunit ... , 12 types, 12 molecules AAgAhAiAjAkAlAmAnAoApAq

#9: Protein Cytochrome c oxidase subunit 6C


Mass: 8617.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TXH1
#53: Protein Cytochrome c oxidase subunit 8


Mass: 7615.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQT4
#54: Protein Cytochrome c oxidase subunit 7A1, mitochondrial


Mass: 9028.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q8SPJ9
#55: Protein Cytochrome c oxidase subunit 7B


Mass: 9169.476 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BJ57
#56: Protein Cytochrome c oxidase subunit 7C, mitochondrial


Mass: 7358.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1W0Y2
#57: Protein Cytochrome c oxidase subunit 1


Mass: 56992.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79876
#58: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 26203.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P50667, cytochrome-c oxidase
#59: Protein Cytochrome c oxidase subunit 3


Mass: 29753.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35916
#60: Protein Cytochrome c oxidase subunit 4


Mass: 19670.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T8J9
#61: Protein Cytochrome c oxidase subunit 5A, mitochondrial


Mass: 16771.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJ34
#62: Protein Cytochrome c oxidase subunit 5B, mitochondrial


Mass: 13801.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q5S3G4
#63: Protein Cytochrome c oxidase subunit 6A2


Mass: 10876.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEB7

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 10 molecules abcdenopZt

#10: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial


Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#11: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15603.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UIV8
#12: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21702.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7
#13: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0R7A9
#14: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYI7
#22: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 7044.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SNY5
#23: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4


Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 26347.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#47: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 12857.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0INK7
#50: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 16487.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules fg

#15: Protein NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial


Mass: 8664.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYQ2
#16: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14327.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules hCDFHIJ

#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5


Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VX77
#28: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial


Mass: 53282.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480XQH6
#29: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Complex I-30kD / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 30241.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNN4
#31: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13348.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1THU2
#32: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / Complex I-23kD / NADH-ubiquinone oxidoreductase 23 kDa subunit


Mass: 23893.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZUN9
#33: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit


Mass: 29235.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VTL7
#34: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 19718.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: G8IFA6

+
NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijkmqrl

#18: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating)
#19: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 12998.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79880
#20: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating)
#21: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79882
#25: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51859.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79881, NADH:ubiquinone reductase (H+-translocating)
#26: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79874, NADH:ubiquinone reductase (H+-translocating)
#48: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68695.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q9TDR1, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules BER

#27: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50637.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SZP7
#30: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 27439.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VRV3
#40: Protein NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Complex I-9kD / NADH-ubiquinone oxidoreductase 9 kDa subunit


Mass: 12172.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480TFA5

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 11 types, 11 molecules KNPQSTUVsLM

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


Mass: 17162.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#36: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1


Mass: 13321.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0UWW0
#38: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11099.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1FN21
#39: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 17889.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0Z0K9
#41: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 8034.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0TJQ4
#42: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 18319.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VPG4
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#44: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#49: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-19kD / NADH-ubiquinone oxidoreductase 19 kDa subunit


Mass: 27760.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1
#66: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 42066.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL07
#67: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7


Mass: 12648.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8W4F7N8

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NADH:ubiquinone oxidoreductase subunit ... , 2 types, 2 molecules WY

#45: Protein NADH:ubiquinone oxidoreductase subunit A13


Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K655
#46: Protein NADH:ubiquinone oxidoreductase subunit B2


Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1G9F4

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Non-polymers , 8 types, 21 molecules

#68: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#69: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#70: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#71: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#72: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#73: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#74: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#75: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3

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Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

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Sample preparation

ComponentName: Cryo-EM structure of respiratory supercomplex I+III2 / Type: COMPLEX
Entity ID: #9, #50, #31, #35, #43, #47, #10, #18, #21, #24-#25, #52, #4, #53-#64, #1-#3, #51, #5-#8, #27-#30, #65, #32-#34, #66-#67, #36-#39, #42, #44, #41
Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6754 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004115805
ELECTRON MICROSCOPYf_angle_d0.717157315
ELECTRON MICROSCOPYf_dihedral_angle_d13.61842439
ELECTRON MICROSCOPYf_chiral_restr0.10617225
ELECTRON MICROSCOPYf_plane_restr0.00419903

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