[English] 日本語
Yorodumi
- PDB-5gpn: Architecture of mammalian respirasome -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
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 / homologyNADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Ubiquinol-cytochrome C reductase hinge domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase-like, subunit I superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily ...NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Ubiquinol-cytochrome C reductase hinge domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase-like, subunit I superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit 8 superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-quinone oxidoreductase, subunit D superfamily / Cytochrome c oxidase, subunit VIa superfamily / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Phosphopantetheine attachment site / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Molybdopterin oxidoreductase / Proton-conducting membrane transporter / Rieske [2Fe-2S] domain / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6/petB / Cytochrome b(C-terminal)/b6/petD / Cytochrome c oxidase subunit VII / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / Cytochrome c oxidase, subunit VIIa superfamily / NAD(P)-binding domain superfamily / Insulinase (Peptidase family M16) / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / Cytochrome c oxidase, subunit Vb, zinc binding site / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / Soluble ligand binding domain / Zinc finger, CHCC-type / NADH-ubiquinone oxidoreductase, subunit 10 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NAD(P)H-quinone oxidoreductase subunit D/H / Cytochrome c oxidase, subunit VIa, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Rieske [2Fe-2S] iron-sulphur domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Di-haem cytochrome, transmembrane / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Cytochrome c1, transmembrane anchor, C-terminal / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Deoxynucleoside kinase domain / Thioredoxin-like superfamily / Cytochrome b/b6, C-terminal domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit I domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Protein MGARP, N-terminal / Cytochrome b / Cytochrome C oxidase, subunit VIIB domain superfamily / Single alpha-helix domain superfamily / [NiFe]-hydrogenase, large subunit / Cytochrome b/b6-like domain superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Protein MGARP / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH ubiquinone oxidoreductase, 20 Kd subunit / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Cytochrome c oxidase subunit VIa signature. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Cytochrome oxidase subunit I profile. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Insulinase family, zinc-binding region signature. / CO II and nitrous oxide reductase dinuclear copper centers signature. / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Phosphopantetheine attachment site. / Carrier protein (CP) domain profile. / Cytochrome oxidase subunit II copper A binding domain profile. / NADH dehydrogenase 1 alpha subcomplex subunit 3 / Respiratory electron transport / Thioredoxin-like [2Fe-2S] ferredoxin / Tim17/Tim22/Tim23/Pmp24 family
Function and homology information
Specimen sourceBos taurus (cattle)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.4 Å resolution
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
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9534
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

+
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 (cattle) / 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 (cattle) / 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 (cattle) / References: 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 (cattle)
#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 (cattle) / 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 (cattle) / 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 (cattle)
References: UniProt: P13272, 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 (cattle) / 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 (cattle) / References: UniProt: P07552

+
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 (cattle) / 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 (cattle) / References: UniProt: P00125
#13: Protein/peptide NADH-ubiquinone oxidoreductase 75 kDa subunit


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


Mass: 17326.223 Da / Num. of mol.: 2 / Source: (natural) Sus scrofa (pig) / 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 (pig) / References: UniProt: G8IFA6

+
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 (pig) / 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 (pig) / 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 (pig) / 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 (pig)
#28: 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
#35: 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

+
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 (pig) / References: UniProt: F1RVN1
#18: Protein/peptide NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


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

+
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 (pig)
References: UniProt: O79874, 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 (pig)
References: UniProt: O79875, 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 (pig)
References: UniProt: O79880, 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 (pig)
References: UniProt: O79881, 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 (pig)
References: UniProt: P56632, 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 (pig)
References: UniProt: Q9TDR1, 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 (pig)
References: UniProt: O79882, NADH dehydrogenase (ubiquinone)

+
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 (pig) / 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 (pig) / References: 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 (pig) / 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 (pig) / 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 (pig) / 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 (pig) / 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 (pig) / 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 (pig) / 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 (pig) / 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 (pig) / References: UniProt: F1SLR1

+
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 (pig) / 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 (pig) / 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 (pig) / References: UniProt: K7GSE5

+
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 (cattle)
#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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / 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 (cattle) / References: UniProt: P00396, 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 (cattle) / References: UniProt: P68530

+
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 (pig)
#51: Protein/peptide
NADH dehydrogenase [ubiquinone] 1 unknown subunit fragment


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


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


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


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


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

+
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 (pig) / References: UniProt: F1STY1
#58: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1


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

+
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 / Iron–sulfur cluster
#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

+
Details

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

-
Experimental details

-
Experiment

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

-
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 MDa / Experimental value: YES
Source (natural)Organism: Sus scrofa (pig)
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

-
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 FIELDBright-field microscopy
Image recordingElectron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k)

-
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
12EMAN2.13D reconstruction
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

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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