[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 / homologyThioredoxin-like [2Fe-2S] ferredoxin / Ubiquinol-cytochrome C reductase hinge domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome bc1 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 ...Thioredoxin-like [2Fe-2S] ferredoxin / Ubiquinol-cytochrome C reductase hinge domain superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / Cytochrome bc1 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 / Cytochrome C oxidase subunit II, periplasmic domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Molybdopterin oxidoreductase / Proton-conducting membrane transporter / Rieske [2Fe-2S] domain / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase / Cytochrome C and Quinol oxidase polypeptide I / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / Cytochrome b/b6/petB / Cytochrome b(C-terminal)/b6/petD / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / 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 / Phosphopantetheine attachment site / 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] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Di-haem cytochrome, transmembrane / 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/plastoquinone oxidoreductase, chain 3 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain G, C-terminal / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / 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 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Cytochrome c oxidase subunit VIa signature. / 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. / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase 1 alpha subcomplex subunit 3 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Carrier protein (CP) domain profile. / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / 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: quinol-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, quinol-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:ubiquinone reductase (H+-translocating)
#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:ubiquinone reductase (H+-translocating)
#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:ubiquinone reductase (H+-translocating)
#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:ubiquinone reductase (H+-translocating)
#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:ubiquinone reductase (H+-translocating)
#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:ubiquinone reductase (H+-translocating)
#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:ubiquinone reductase (H+-translocating)

+
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:ubiquinone reductase (H+-translocating)
#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

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

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

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

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

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. 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

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