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- PDB-5gup: Cryo-EM structure of mammalian respiratory supercomplex I1III2IV1 -

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Database: PDB / ID: 5gup
TitleCryo-EM structure of mammalian respiratory supercomplex I1III2IV1
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein, mitochondrial
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsELECTRON TRANSPORT / Cryo-EM / Mammalian / Respiratory / Supercomplex
Function / homologyTim17/Tim22/Tim23/Pmp24 family / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / ACP-like superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily ...Tim17/Tim22/Tim23/Pmp24 family / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / ACP-like superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6/petB / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Rieske [2Fe-2S] domain / Proton-conducting membrane transporter / Molybdopterin oxidoreductase / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Cytochrome b/b6, C-terminal domain superfamily / Protein MGARP, N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Rieske [2Fe-2S] iron-sulphur domain / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH-ubiquinone oxidoreductase, subunit 10 / Deoxynucleoside kinase domain / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NAD(P)H-quinone oxidoreductase subunit D/H / Ubiquinol-cytochrome C reductase hinge domain / Protein MGARP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Cytochrome b/b6-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / [NiFe]-hydrogenase, large subunit / Single alpha-helix domain superfamily / Cytochrome b / Phosphopantetheine attachment site / Insulinase (Peptidase family M16) / Cytochrome b-c1 complex subunit 10 / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH dehydrogenase 1 beta subcomplex subunit 2 / Mitochondria Localisation Sequence / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH-ubiquinone oxidoreductase MWFE subunit / Phosphopantetheine attachment site. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Zinc-finger domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Carrier protein (CP) domain profile. / Cytochrome b/b6 N-terminal region profile. / Cytochrome b/b6 C-terminal region profile. / Rieske [2Fe-2S] iron-sulfur domain profile. / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Thioredoxin-like [2Fe-2S] ferredoxin / SLBB domain / NADH-ubiquinone oxidoreductase subunit 10 / NADH ubiquinone oxidoreductase, 20 Kd subunit / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / NADH-ubiquinone oxidoreductase chain 4, amino terminus / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Deoxynucleoside kinase / Cytochrome c oxidase subunit Va / Ubiquinol-cytochrome C reductase hinge protein / Ubiquinol cytochrome reductase transmembrane region
Function and homology information
Specimen sourceSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsGu, J. / Wu, M. / Guo, R. / Yang, M.
CitationJournal: Cell / Year: 2016
Title: Structure of Mammalian Respiratory Supercomplex IIIIIV.
Authors: Meng Wu / Jinke Gu / Runyu Guo / Yushen Huang / Maojun Yang
Abstract: The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to ...The mammalian respiratory chain complexes assemble into supercomplexes (SCs) and reside in the inner mitochondrial membrane to transfer electrons and establish the proton gradient for complex V to synthesize ATP. The precise arrangement of SCs is largely unknown. Here, we report a 4.0-Å cryo-electron microscopy (cryo-EM) structure of the major SC in porcine heart, the 1.7-MDa SCIIIIIV. The complex III (CIII) dimer and complex IV (CIV) bind at the same side of the L-shaped complex I (CI). Several accessory or supernumerary subunits of CI, such as NDUFA11, NDUFB4, NDUFB8, and NDUFB9, directly contribute to the oligomerization of CI, CIII, and CIV. COX7C and COX7A of CIV attach CIV to the concave surface formed by CIII and the distal end of membrane arm of CI. The structure suggests a possible mechanism by which electrons are transferred from NADH to cytochrome c and provides a platform for future functional dissection of respiration.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 30, 2016 / Release: Mar 29, 2017

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 6C
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
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
K: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
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
O: Acyl carrier protein, mitochondrial
P: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
R: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
X: Acyl carrier protein, mitochondrial
Y: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
Z: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
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
l: NADH-ubiquinone oxidoreductase chain 5
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
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, heme protein, mitochondrial
y: Cytochrome b-c1 complex subunit 7
z: Cytochrome b-c1 complex subunit 8
0: Cytochrome b-c1 complex subunit 6, mitochondrial
1: Cytochrome b-c1 complex subunit 9
2: Cytochrome b-c1 complex subunit Rieske, mitochondrial
3: Cytochrome b-c1 complex subunit 10
4: Cytochrome b-c1 complex subunit Rieske, mitochondrial
5: Cytochrome b-c1 complex subunit 1, mitochondrial
6: Cytochrome b-c1 complex subunit 2, mitochondrial
7: Cytochrome b
8: Cytochrome c1, heme protein, mitochondrial
9: Cytochrome b-c1 complex subunit 7
Aa: Cytochrome b-c1 complex subunit 8
Ab: Cytochrome b-c1 complex subunit 6, mitochondrial
Ac: Cytochrome b-c1 complex subunit 9
Ad: Cytochrome b-c1 complex subunit 10
Ae: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Af: Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial
Ag: Cytochrome c oxidase subunit 8B, mitochondrial
Ah: Cytochrome c oxidase subunit 7A1, mitochondrial
Ai: Cytochrome c oxidase subunit 7B, mitochondrial
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 isoform 1, mitochondrial
Ao: Cytochrome c oxidase subunit 5A, mitochondrial
Ap: Cytochrome c oxidase subunit 5B, mitochondrial
Aq: Cytochrome c oxidase subunit 6A, mitochondrial
Ar: Cytochrome c oxidase subunit 6B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,818,749132
Polyers1,781,94180
Non-polymers36,80852
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Cytochrome c oxidase subunit ... , 13 types, 13 molecules AAgAhAiAjAkAlAmAnAoApAqAr

#1: Protein/peptide Cytochrome c oxidase subunit 6C /


Mass: 8494.982 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#56: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial /


Mass: 4967.756 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#57: Protein/peptide Cytochrome c oxidase subunit 7A1, mitochondrial /


Mass: 6682.726 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#58: Protein/peptide Cytochrome c oxidase subunit 7B, mitochondrial /


Mass: 6365.217 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#59: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial /


Mass: 5449.396 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#60: Protein/peptide Cytochrome c oxidase subunit 1 /


Mass: 57065.844 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#61: Protein/peptide Cytochrome c oxidase subunit 2 /


Mass: 26040.393 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#62: Protein/peptide Cytochrome c oxidase subunit 3 /


Mass: 29943.600 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#63: Protein/peptide Cytochrome c oxidase subunit 4 isoform 1, mitochondrial /


Mass: 17179.646 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#64: Protein/peptide Cytochrome c oxidase subunit 5A, mitochondrial /


Mass: 12453.081 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJ34
#65: Protein/peptide Cytochrome c oxidase subunit 5B, mitochondrial /


Mass: 10684.038 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#66: Protein/peptide Cytochrome c oxidase subunit 6A, mitochondrial /


Mass: 9452.687 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#67: Protein/peptide Cytochrome c oxidase subunit 6B1 /


Mass: 10039.244 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules BE

#2: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50637.766 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RVN1
#5: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 26301.637 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SM98

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

#3: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial


Mass: 52552.301 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S1A8
#4: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial


Mass: 30241.416 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIF2
#6: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13348.950 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S031
#8: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial


Mass: 23893.281 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)
#9: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 23777.742 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LK43
#10: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 19718.500 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: G8IFA6
#32: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 5


Mass: 12506.591 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SV23

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Protein/peptide , 4 types, 7 molecules GOXw7x8

#7: Protein/peptide NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 79627.398 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SHD7
#15: Protein/peptide Acyl carrier protein, mitochondrial


Mass: 17326.223 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SAB6
#47: Protein/peptide Cytochrome b /


Mass: 42840.715 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1HBG9
#48: Protein/peptide Cytochrome c1, heme protein, mitochondrial /


Mass: 35488.930 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig)

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 13 molecules KRLMNPQSTUVWs

#11: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17162.439 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#12: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial


Mass: 42606.324 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL07
#13: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7


Mass: 12648.590 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SA62
#14: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5


Mass: 13321.590 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLY2
#16: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11099.798 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RGE3
#17: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 14953.313 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRG2
#18: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 8088.424 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GR43
#19: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3


Mass: 9225.567 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNI5
#20: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#21: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14686.894 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#22: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16911.611 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S6Q1
#43: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20064.096 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopt

#23: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial


Mass: 11939.366 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SRQ0
#24: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3


Mass: 11128.515 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SI50
#25: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial


Mass: 21587.006 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#26: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6


Mass: 15603.177 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN80
#27: Protein/peptide 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: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7
#28: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 20944.768 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LDC3
#29: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 17384.729 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWV4
#38: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1


Mass: 7044.278 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SD73
#39: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4


Mass: 15117.350 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LPW0
#40: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 21864.906 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#44: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 16487.887 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig)

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

#30: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial


Mass: 8630.037 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRC9
#31: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14327.655 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1STY1

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmqr

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


Mass: 39077.504 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: O79875
#34: Protein/peptide NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12998.448 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: O79880
#35: Protein/peptide NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: P56632
#36: Protein/peptide NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68695.500 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: Q9TDR1
#37: Protein/peptide NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19021.332 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: O79882
#41: Protein/peptide NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51859.387 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: O79881
#42: Protein/peptide NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35667.520 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / References: UniProt: O79874

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Cytochrome b-c1 complex subunit ... , 9 types, 18 molecules u5v6y9zAa0Ab1Ac243AdAeAf

#45: Protein/peptide Cytochrome b-c1 complex subunit 1, mitochondrial


Mass: 52756.320 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKM0
#46: Protein/peptide Cytochrome b-c1 complex subunit 2, mitochondrial


Mass: 48264.477 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig)
#49: Protein/peptide Cytochrome b-c1 complex subunit 7


Mass: 13587.549 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig)
#50: Protein/peptide Cytochrome b-c1 complex subunit 8


Mass: 9784.339 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI18
#51: Protein/peptide Cytochrome b-c1 complex subunit 6, mitochondrial


Mass: 10685.803 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S3W0
#52: Protein/peptide Cytochrome b-c1 complex subunit 9


Mass: 7412.530 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN79
#53: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 29492.600 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNZ1
#54: Protein/peptide Cytochrome b-c1 complex subunit 10


Mass: 6560.654 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SDI2
#55: Protein/peptide Cytochrome b-c1 complex subunit Rieske transit peptide, mitochondrial


Mass: 7900.107 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNZ1

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Non-polymers , 14 types, 52 molecules

#68: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Formula: Fe4S4 / Iron–sulfur cluster
#69: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Formula: C17H21N4O9P / Flavin mononucleotide
#70: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Formula: Fe2S2
#71: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 5 / Formula: C42H89NO8P
#72: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Formula: C21H30N7O17P3
#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.: 2 / Formula: C25H49N2O8PS
#74: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 10 / Formula: C81H156O17P2 / Cardiolipin / Comment: phospholipid *YM
#75: Chemical
ChemComp-PEE / 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 749.073 Da / Num. of mol.: 10 / Formula: C41H83NO8P / Discrete optimized protein energy / Comment: DOPE (phospholipid) *YM
#76: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / Heme
#77: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Formula: C34H34FeN4O4 / Heme C
#78: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Formula: C49H56FeN4O6 / Heme A
#79: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Formula: Cu / Copper
#80: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#81: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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Details

Sequence detailsTHE SEQUENCE OF RESIDUE 1-47 OF CHAIN E IS MFLTAALRARATGFTAQWGRHVRNLHKTAVQNGAGGALFVHRDTPEN. THE ...THE SEQUENCE OF RESIDUE 1-47 OF CHAIN E IS MFLTAALRARATGFTAQWGRHVRNLHKTAVQNGAGGALFVHRDTPEN. THE AUTHOR COULD OBSERVE SOME CONNECTED RESIDUES AND ASSIGNED UNK TO THESE RESIDUES. THE AUTHOR IS NOT SURE WHCIH PART OF RESIDUE 1-47 CORRESPONDS WITH THIS PEPTIDE OF UNK. SO THE RESIDUE NUMBERS OF UNK IS MEANINGLESS.

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Respiratory supercomplex I1III2IV1 / Type: COMPLEX / Details: Supercomplex generated by complex I, III and IV.
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67
Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: YES
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1particle selection
2AutoEMation2.0image acquisition
4CTFFIND3.0CTF correction
7COOT0.8.2model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIX1.9model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 161912 / Symmetry type: POINT

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