[English] 日本語
Yorodumi
- PDB-9buh: Cryo-EM structure of respiratory supercomplex I III IV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9buh
TitleCryo-EM structure of respiratory supercomplex I III IV
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 / respiratory chain complex IV assembly / Mitochondrial protein import / subthalamus development / pons development / : / mitochondrial respirasome assembly ...Complex IV assembly / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Complex III assembly / respiratory chain complex IV assembly / Mitochondrial protein import / subthalamus development / pons development / : / mitochondrial respirasome assembly / RHOG GTPase cycle / cerebellar Purkinje cell layer development / mitochondrial respiratory chain complex III assembly / Complex I biogenesis / Respiratory electron transport / pyramidal neuron development / respiratory chain complex IV / thalamus development / Mitochondrial protein degradation / Neutrophil degranulation / mesenchymal stem cell proliferation / reproductive system development / respiratory chain complex / cytochrome-c oxidase / respiratory chain complex III / mesenchymal stem cell differentiation / circulatory system development / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cardiac muscle tissue development / 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 ATP synthesis coupled electron transport / 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 / reactive oxygen species metabolic process / muscle contraction / aerobic respiration / central nervous system development / regulation of mitochondrial membrane potential / respiratory electron transport chain / hippocampus development / DNA damage response, signal transduction by p53 class mediator / kidney development / electron transport chain / fatty acid metabolic process / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / multicellular organism growth / NAD binding / fatty acid biosynthetic process / cellular senescence / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / gene expression / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / nuclear body / mitochondrial matrix / copper ion binding / heme binding / protein-containing complex / 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 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome oxidase c subunit VIII / 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 Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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 b-c1 complex subunit 7 / Cytochrome c oxidase subunit III-like superfamily / 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 / Cytochrome b-c1 complex subunit 9 / 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 c/quinol oxidase subunit II / : / Cytochrome b / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / 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. / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / : / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1
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] 1 beta subcomplex subunit 6 / 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 / 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 alpha subcomplex subunit 3 / 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: 2.8 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: Cryo-EM structure of respiratory supercomplex I III IV
Authors: Zhang, Z. / Maharjan, R. / Tringides, M.
History
DepositionMay 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c oxidase subunit 6C
t: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
F: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
K: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
U: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
a: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
i: NADH-ubiquinone oxidoreductase chain 2
m: NADH-ubiquinone oxidoreductase chain 6
p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
q: NADH-ubiquinone oxidoreductase chain 4
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
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
5: Cytochrome b-c1 complex subunit 1, mitochondrial
6: Cytochrome b-c1 complex subunit 2, mitochondrial
7: Cytochrome b
8: Cytochrome c1
9: Cytochrome b-c1 complex subunit 7
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
G: NADH-ubiquinone oxidoreductase 75 kDa subunit, 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
L: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
M: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
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
S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
T: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
W: NADH:ubiquinone oxidoreductase subunit A13
Y: NADH:ubiquinone oxidoreductase subunit B2
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
j: NADH-ubiquinone oxidoreductase chain 3
k: NADH-ubiquinone oxidoreductase chain 4L
l: NADH-ubiquinone oxidoreductase chain 5
n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
r: NADH-ubiquinone oxidoreductase chain 1
s: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
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
X: Acyl carrier protein
R: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
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)1,900,307101
Polymers1,890,31480
Non-polymers9,99221
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

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

#1: Protein Cytochrome c oxidase subunit 6C


Mass: 8626.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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

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

#2: 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
#6: 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
#7: 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
#10: 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
#53: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Complex I-B17 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 21904.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480KM09
#54: 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
#55: 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
#56: 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
#63: 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
#64: 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

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

#3: 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
#35: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / Complex I-49kD / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 53282.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480XQH6
#36: 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
#39: 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
#40: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 28500.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VVS8
#41: 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
#59: 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

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

#4: 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
#5: 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
#42: 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
#43: 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
#44: 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
#46: 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
#47: 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
#48: 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
#49: 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: A0A8D0Q6N1
#50: 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
#66: 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

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

#8: 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)
#9: 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
#11: 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)
#60: 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
#61: 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)
#62: 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)
#65: 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)

+
Cytochrome b-c1 complex subunit ... , 6 types, 12 molecules AazAb0Ad35u6v9y

#12: 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
#13: 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
#15: 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
#29: 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
#30: 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
#33: 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

+
Ubiquinol-cytochrome c ... , 2 types, 6 molecules Ac124AeAf

#14: 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
#28: 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

+
Protein , 5 types, 8 molecules Ar7w8xGOX

#27: 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
#31: 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
#32: 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
#38: 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
#45: 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

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

#34: 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
#37: 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
#67: 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

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

#51: 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
#52: 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

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

#57: 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
#58: 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

+
Non-polymers , 8 types, 21 molecules

#68: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#69: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


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


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


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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#74: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#75: 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

+
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of respiratory supercomplex I III IV
Type: COMPLEX / Entity ID: #1-#12, #15-#27, #13-#14, #28-#67 / 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

-
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)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: OTHER / Num. of particles: 54742 / 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more