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- PDB-5gpn: Architecture of mammalian respirasome -

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Database: PDB / ID: 5gpn
TitleArchitecture of mammalian respirasome
Components
  • (Cytochrome b-c1 complex subunit ...) x 9
  • (Cytochrome c oxidase subunit ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 10
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 3
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 unknown subunit ...) x 6
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 6
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • Mitochondrial NADH dehydrogenase Fe-S protein 4
  • NADH-ubiquinone oxidoreductase 75 kDa subunit
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / Respiratory / Respirasome / Mammalian
Function/homologyMitochondrial Fatty Acid Beta-Oxidation / Protein MGARP, N-terminal / Protein MGARP / Mitochondria Localisation Sequence / Complex I biogenesis / Respiratory electron transport / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24 / ubiquinone-6 biosynthetic process / Glyoxylate metabolism and glycine degradation ...Mitochondrial Fatty Acid Beta-Oxidation / Protein MGARP, N-terminal / Protein MGARP / Mitochondria Localisation Sequence / Complex I biogenesis / Respiratory electron transport / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Mitochondrial inner membrane translocase subunit Tim17/Tim22/Tim23/peroxisomal protein PMP24 / ubiquinone-6 biosynthetic process / Glyoxylate metabolism and glycine degradation / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase, subunit 10 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase subunit 2, C-terminal / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / GRIM-19 / Thioredoxin-like [2Fe-2S] ferredoxin / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Zinc finger, CHCC-type / GRIM-19 protein / reproductive system development / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase, chain M/4 / NADH-plastoquinone oxidoreductase, chain 5 / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH-ubiquinone oxidoreductase subunit 10 / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH dehydrogenase (ubiquinone) / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Complex 1 LYR protein / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase subunit E-like / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH dehydrogenase subunit 5 C-terminus / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH dehydrogenase / NAD(P)H-quinone oxidoreductase subunit D/H / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase MWFE subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Soluble ligand binding domain / mitochondrial respiratory chain complex I / NADH dehydrogenase subunit 2 C-terminus / intrinsic component of mitochondrial membrane / Zinc-finger domain / Single alpha-helix domain superfamily / Cytochrome b-c1 complex subunit 10 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH dehydrogenase / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NmrA-like domain / CHCH / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH dehydrogenase activity / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / Cytochrome c oxidase subunit VII / mitochondrial respiratory chain complex I assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial electron transport, NADH to ubiquinone / pons development / subthalamus development / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV
Function and homology information
Specimen sourceBos taurus / mammal / Cattle /
Sus scrofa / mammal / image: Sus scrofa domestica
MethodElectron microscopy (5.4 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsGu, J. / Wu, M. / Guo, R. / Yang, M.
CitationJournal: Nature / Year: 2016
Title: The architecture of the mammalian respirasome.
Authors: Jinke Gu / Meng Wu / Runyu Guo / Kaige Yan / Jianlin Lei / Ning Gao / Maojun Yang
Abstract: The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing ...The respiratory chain complexes I, III and IV (CI, CIII and CIV) are present in the bacterial membrane or the inner mitochondrial membrane and have a role of transferring electrons and establishing the proton gradient for ATP synthesis by complex V. The respiratory chain complexes can assemble into supercomplexes (SCs), but their precise arrangement is unknown. Here we report a 5.4 Å cryo-electron microscopy structure of the major 1.7 megadalton SCI1III2IV1 respirasome purified from porcine heart. The CIII dimer and CIV bind at the same side of the L-shaped CI, with their transmembrane domains essentially aligned to form a transmembrane disk. Compared to free CI, the CI in the respirasome is more compact because of interactions with CIII and CIV. The NDUFA11 and NDUFB9 supernumerary subunits of CI contribute to the oligomerization of CI and CIII. The structure of the respirasome provides information on the precise arrangements of the respiratory chain complexes in mitochondria.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 3, 2016 / Release: Apr 5, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 5, 2017Structure modelrepositoryInitial release
1.1Apr 12, 2017Structure modelRefinement description

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
L: Cytochrome b-c1 complex subunit 9
M: Cytochrome b-c1 complex subunit 1, mitochondrial
N: Cytochrome b-c1 complex subunit 2, mitochondrial
O: Cytochrome b
P: Cytochrome c1, heme protein, mitochondrial
Q: Cytochrome b-c1 complex subunit Rieske, mitochondrial
R: Cytochrome b-c1 complex subunit 7
S: Cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 6, mitochondrial
U: Cytochrome b-c1 complex subunit Rieske, mitochondrial
V: Cytochrome b-c1 complex subunit 10
W: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
Y: NADH-ubiquinone oxidoreductase 75 kDa subunit
Z: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
a: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7
b: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8
c: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
d: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
e: NADH-ubiquinone oxidoreductase chain 1
f: NADH-ubiquinone oxidoreductase chain 2
g: NADH-ubiquinone oxidoreductase chain 3
h: NADH-ubiquinone oxidoreductase chain 4
i: NADH-ubiquinone oxidoreductase chain 4L
j: NADH-ubiquinone oxidoreductase chain 5
k: NADH-ubiquinone oxidoreductase chain 6
l: NADH-ubiquinone oxidoreductase chain 6
m: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
n: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
o: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
p: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9
q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
t: Acyl carrier protein
u: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
v: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
w: Mitochondrial NADH dehydrogenase Fe-S protein 4
x: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
0: Cytochrome c oxidase subunit 3
1: Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
2: Cytochrome c oxidase subunit 5A, mitochondrial
3: Cytochrome c oxidase subunit 5B, mitochondrial
4: Cytochrome c oxidase subunit 6A2, mitochondrial
5: Cytochrome c oxidase subunit 6B1
6: Cytochrome c oxidase subunit 6C
7: Cytochrome c oxidase subunit 7A1, mitochondrial
8: Cytochrome c oxidase subunit 7B, mitochondrial
9: Cytochrome c oxidase subunit 7C, mitochondrial
s: Cytochrome c oxidase subunit 8B, mitochondrial
y: Cytochrome c oxidase subunit 1
z: Cytochrome c oxidase subunit 2
Aa: Acyl carrier protein
Ab: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ac: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Ad: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ae: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Af: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Ag: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Ah: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ai: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5
Aj: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Ak: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Al: NADH dehydrogenase [ubiquinone] 1 subunit C2
Am: NADH dehydrogenase [ubiquinone] 1 subunit C1
An: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Ao: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ap: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Aq: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Ar: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
As: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
At: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Au: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Av: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
Aw: NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,741,771109
Polyers1,732,06784
Non-polymers9,70425
Water0
1


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

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Components

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

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


Mass: 49266.254 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P31800
#2: Protein/peptide Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 46575.469 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P23004
#5: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 29572.814 Da / Num. of mol.: 2 / Source: (natural) Bos taurus
References: EC:1.10.2.2 (ubiquinol—cytochrome-c reductase)
#6: Protein/peptide Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 13371.190 Da / Num. of mol.: 2 / Source: (natural) Bos taurus
#7: Protein/peptide Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9606.027 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P13271
#8: Protein/peptide Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 9189.116 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P00126
#9: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 7964.259 Da / Num. of mol.: 2 / Source: (natural) Bos taurus
References: UniProt:P13272, EC:1.10.2.2 (ubiquinol—cytochrome-c reductase)
#10: Protein/peptide Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7209.311 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P00130
#11: Protein/peptide Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


Mass: 6527.604 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P07552

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Protein/peptide , 5 types, 8 molecules CODPYtAaw

#3: Protein/peptide Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42620.340 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P00157
#4: Protein/peptide Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt:P00125
#13: Protein/peptide NADH-ubiquinone oxidoreductase 75 kDa subunit


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


Mass: 17326.223 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa / References: UniProt:F1SAB6
#34: Protein/peptide Mitochondrial NADH dehydrogenase Fe-S protein 4


Mass: 19718.500 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:G8IFA6

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 6 types, 6 molecules WZabox

#12: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 3


Mass: 30241.416 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1SIF2
#14: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 2


Mass: 52552.301 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1S1A8
#15: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 7


Mass: 23777.742 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:I3LK43
#16: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 8


Mass: 23893.281 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#28: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 5


Mass: 12506.591 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1SV23
#35: Protein/peptide NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13348.950 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1S031

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

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


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


Mass: 27439.533 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1SM98

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 8 molecules efghijkl

#19: Protein/peptide NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35667.520 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
References: UniProt:O79874, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#20: Protein/peptide NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39077.504 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
References: UniProt:O79875, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#21: Protein/peptide NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12998.448 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
References: UniProt:O79880, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#22: Protein/peptide NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51859.387 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
References: UniProt:O79881, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#23: Protein/peptide NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
References: UniProt:P56632, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#24: Protein/peptide NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68695.500 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
References: UniProt:Q9TDR1, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#25: Protein/peptide NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19021.332 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa
References: UniProt:O79882, EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 11 molecules mnpqvrAcAeAfAgAn

#26: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3


Mass: 9225.567 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1RNI5
#27: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11099.798 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: EC:1.6.5.3 (NADH dehydrogenase (ubiquinone))
#29: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9


Mass: 42606.324 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1SL07
#30: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa / References: UniProt:F1SIS9
#31: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


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


Mass: 8088.424 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:K7GR43
#52: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5


Mass: 13321.590 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1SLY2
#53: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 14953.313 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1SRG2
#54: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14686.894 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:I3LGM4
#59: Protein/peptide NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


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

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 3 types, 4 molecules uAiAjAk

#33: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5


Mass: 21587.006 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa / References: UniProt:F1SGC6
#55: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 20944.768 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:I3LDC3
#56: Protein/peptide NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 21733.711 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:K7GSE5

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Cytochrome c oxidase subunit ... , 13 types, 13 molecules 0123456789syz

#36: Protein/peptide Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 29943.600 Da / Num. of mol.: 1 / Source: (natural) Bos taurus
#37: Protein/peptide Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase polypeptide IV / Cytochrome c oxidase subunit IV isoform 1 / COX IV-1


Mass: 17179.646 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P00423
#38: Protein/peptide Cytochrome c oxidase subunit 5A, mitochondrial


Mass: 12453.081 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 44-152 / Source: (natural) Bos taurus / References: UniProt:P00426
#39: Protein/peptide Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide VIa / Cytochrome c oxidase polypeptide Vb


Mass: 10684.038 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P00428
#40: Protein/peptide Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


Mass: 9452.687 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 13-96 / Source: (natural) Bos taurus / References: UniProt:P07471
#41: Protein/peptide Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase polypeptide VII / Cytochrome c oxidase subunit AED / Cytochrome c oxidase subunit VIb isoform 1 / COX VIb-1


Mass: 10039.244 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P00429
#42: Protein/peptide Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8494.982 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P04038
#43: Protein/peptide Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit VIIIc / VIIIC / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H / Cytochrome c oxidase subunit VIIa-muscle / Cytochrome c oxidase subunit VIIa-M


Mass: 6682.726 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P07470
#44: Protein/peptide Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb / IHQ


Mass: 6365.217 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P13183
#45: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIIA / Cytochrome c oxidase polypeptide VIIc


Mass: 5449.396 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P00430
#46: Protein/peptide Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase polypeptide VIII-heart / Cytochrome c oxidase subunit 8-1 / Cytochrome c oxidase subunit 8H / IX / VIIIb


Mass: 4967.756 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P10175
#47: Protein/peptide Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 57065.844 Da / Num. of mol.: 1 / Source: (natural) Bos taurus
References: UniProt:P00396, EC:1.9.3.1 (cytochrome-c oxidase)
#48: Protein/peptide Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 26040.393 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt:P68530

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NADH dehydrogenase [ubiquinone] 1 unknown subunit ... , 6 types, 12 molecules AbAhAdAoApAvAqAsAwArAtAu

#49: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 11422.071 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa
#51: Protein/peptide
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 3677.524 Da / Num. of mol.: 4 / Source: (natural) Sus scrofa
#60: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 6485.986 Da / Num. of mol.: 3 / Source: (natural) Sus scrofa
#61: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 2911.580 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#62: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 1464.797 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa
#63: Protein/peptide NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


Mass: 1124.378 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa

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

#57: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14327.655 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1STY1
#58: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1


Mass: 8630.037 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt:F1RRC9

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Non-polymers , 10 types, 25 molecules

#64: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 618.503 Da / Num. of mol.: 2 / Formula: C34H34FeN4O4 / : Heme C
#66: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Formula: Fe2S2
#67: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Formula: Fe4S4
#68: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Formula: C17H21N4O9P / : Flavin mononucleotide
#69: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Formula: C21H30N7O17P3
#70: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / : Zinc
#71: Chemical ChemComp-HEA / HEME-A


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


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


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / : Magnesium

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Details

Sequence detailsAuthor does not know the sequences of chains Ab, Ah, Ad, Ao, Ap, Av, Aq, As, Aw, Ar, At, Au

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Respirasome / Type: COMPLEX / Details: Mammalian, respirasome
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, 68, 69, 70, 71, 72, 73
Source: NATURAL
Molecular weightValue: 1.7 deg. / Units: MEGADALTONS / Experimental value: YES
Source (natural)Organism: Sus scrofa
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1EMAN2.1PARTICLE SELECTION
2RELION1.4IMAGE ACQUISITION
4CTFFIND3CTF CORRECTION
7COOT8.01MODEL FITTING
9EMAN2.1INITIAL EULER ASSIGNMENT
10EMAN2.1FINAL EULER ASSIGNMENT
11EMAN2.1CLASSIFICATION
12EMAN2.1RECONSTRUCTION
13PHENIX1.9MODEL REFINEMENT
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 139996 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

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