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- PDB-9bpb: Tethered respiratory III2IV2 supercomplex from Saccharomyces cere... -

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Basic information

Entry
Database: PDB / ID: 9bpb
TitleTethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • (Cytochrome c oxidase subunit ...) x 11
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsELECTRON TRANSPORT / Complex / Oxidoreductase / Respiration
Function / homology
Function and homology information


Complex III assembly / : / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV ...Complex III assembly / : / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV / cellular respiration / respiratory chain complex / cytochrome-c oxidase / respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / ubiquinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / nuclear periphery / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / membrane / cytosol
Similarity search - Function
Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb ...Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile.
Similarity search - Domain/homology
Chem-6PH / Chem-8PE / Chem-9PE / CARDIOLIPIN / Chem-CN3 / Chem-CN5 / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A ...Chem-6PH / Chem-8PE / Chem-9PE / CARDIOLIPIN / Chem-CN3 / Chem-CN5 / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / PHOSPHATIDYLETHANOLAMINE / Chem-UQ6 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 8, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8, mitochondrial / Cytochrome c oxidase subunit 7, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial / Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome b-c1 complex subunit 10, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 26, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsEldeeb, M.H. / Carlstrom, A. / Berndtsson, J. / Ott, M. / Fontanesi, F.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W911NF-21-1-0359 United States
CitationJournal: To Be Published
Title: Differential substrate utilization by yeast respiratory supercomplexes
Authors: Eldeeb, M.H. / Cosner, Z. / Mays, J. / Carlstrom, A. / Rodriguez, G. / Berndtsson, J. / Ott, M. / Fontanesi, F.
History
DepositionMay 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 6, mitochondrial
G: Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial
H: Cytochrome b-c1 complex subunit 8, mitochondrial
I: Cytochrome b-c1 complex subunit 9, mitochondrial
J: Cytochrome b-c1 complex subunit 10, mitochondrial
a: Cytochrome c oxidase subunit 1
b: Cytochrome c oxidase subunit 2
c: Cytochrome c oxidase subunit 3
d: Cytochrome c oxidase subunit 4, mitochondrial
e: Cytochrome c oxidase subunit 5A, mitochondrial
f: Cytochrome c oxidase subunit 6, mitochondrial
g: Cytochrome c oxidase subunit 7, mitochondrial
i: Cytochrome c oxidase subunit 9, mitochondrial
j: Cytochrome c oxidase subunit 12, mitochondrial
k: Cytochrome c oxidase subunit 13, mitochondrial
l: Cytochrome c oxidase subunit 26, mitochondrial
K: Cytochrome b-c1 complex subunit 1, mitochondrial
L: Cytochrome b-c1 complex subunit 2, mitochondrial
M: Cytochrome b
N: Cytochrome c1, heme protein, mitochondrial
O: Cytochrome b-c1 complex subunit Rieske, mitochondrial
P: Cytochrome b-c1 complex subunit 6, mitochondrial
Q: Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial
R: Cytochrome b-c1 complex subunit 8, mitochondrial
S: Cytochrome b-c1 complex subunit 9, mitochondrial
T: Cytochrome b-c1 complex subunit 10, mitochondrial
m: Cytochrome c oxidase subunit 1
n: Cytochrome c oxidase subunit 2
o: Cytochrome c oxidase subunit 3
p: Cytochrome c oxidase subunit 4, mitochondrial
q: Cytochrome c oxidase subunit 5A, mitochondrial
r: Cytochrome c oxidase subunit 6, mitochondrial
s: Cytochrome c oxidase subunit 7, mitochondrial
u: Cytochrome c oxidase subunit 9, mitochondrial
v: Cytochrome c oxidase subunit 12, mitochondrial
w: Cytochrome c oxidase subunit 13, mitochondrial
x: Cytochrome c oxidase subunit 26, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)990,972109
Polymers945,35542
Non-polymers45,61767
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Cytochrome b-c1 complex subunit ... , 8 types, 16 molecules AKBLEOFPGQHRISJT

#1: Protein Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome c oxidoreductase core protein 1 / ...Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome c oxidoreductase core protein 1 / Ubiquinol-cytochrome c reductase 44 kDa protein


Mass: 50282.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07256
#2: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome c oxidoreductase core protein 2


Mass: 40528.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07257
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c oxidoreductase ...Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c oxidoreductase iron-sulfur subunit


Mass: 23393.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VI / Cytochrome c1 non-heme 17 kDa protein / ...Complex III subunit 6 / Complex III subunit VI / Cytochrome c1 non-heme 17 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c oxidoreductase subunit 6 / Ubiquinol-cytochrome c reductase 17 kDa protein


Mass: 17276.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00127
#7: Protein Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial / Complex III subunit 7 / Complex III subunit VII / Ubiquinol-cytochrome c oxidoreductase subunit 7 / ...Complex III subunit 7 / Complex III subunit VII / Ubiquinol-cytochrome c oxidoreductase subunit 7 / Ubiquinol-cytochrome c reductase 14 kDa protein / Cytochrome c oxidase polypeptide VIII


Mass: 20618.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion protein composed of ubiquinol-cytochrome c oxidoreductase subunit 7 (Qcr7) fused by a linker (GGGGS) to a copy of cytochrome c oxidase subunit 8 (Cox8) without its mitochondrial ...Details: Fusion protein composed of ubiquinol-cytochrome c oxidoreductase subunit 7 (Qcr7) fused by a linker (GGGGS) to a copy of cytochrome c oxidase subunit 8 (Cox8) without its mitochondrial targeting sequence.,Fusion protein composed of ubiquinol-cytochrome c oxidoreductase subunit 7 (Qcr7) fused by a linker (GGGGS) to a copy of cytochrome c oxidase subunit 8 (Cox8) without its mitochondrial targeting sequence.
Source: (gene. exp.) Saccharomyces cerevisiae W303 (yeast)
Gene: QCR7, CRO1, UCR7, YDR529C, D9719.32, COX8, YLR395C, L8084.14
Production host: Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00128, UniProt: P04039
#8: Protein Cytochrome b-c1 complex subunit 8, mitochondrial / Complex III subunit 8 / Complex III subunit VII / Ubiquinol-cytochrome c oxidoreductase subunit 8 / ...Complex III subunit 8 / Complex III subunit VII / Ubiquinol-cytochrome c oxidoreductase subunit 8 / Ubiquinol-cytochrome c reductase complex 11 kDa protein / Ubiquinone-binding protein QP-C


Mass: 10987.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P08525
#9: Protein Cytochrome b-c1 complex subunit 9, mitochondrial / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7.3 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7.3 kDa protein / Ubiquinol-cytochrome c oxidoreductase subunit 9 / Ubiquinol-cytochrome c reductase 7.3 kDa protein


Mass: 7485.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P22289
#10: Protein Cytochrome b-c1 complex subunit 10, mitochondrial / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c oxidoreductase subunit 10 ...Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c oxidoreductase subunit 10 / Ubiquinol-cytochrome c reductase 8.5 kDa protein


Mass: 8602.913 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P37299

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Protein , 2 types, 4 molecules CMDN

#3: Protein Cytochrome b / Complex III subunit 3 / Complex III subunit CYTB / Complex III subunit III / Cytochrome b-c1 ...Complex III subunit 3 / Complex III subunit CYTB / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Cytochrome b-c1 complex subunit CYTB / Ubiquinol-cytochrome c oxidoreductase complex cytochrome b subunit


Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00163, quinol-cytochrome-c reductase
#4: Protein Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome c oxidoreductase cytochrome c1 subunit / Cytochrome c-1


Mass: 34097.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07143, quinol-cytochrome-c reductase

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Cytochrome c oxidase subunit ... , 11 types, 22 molecules ambncodpeqfrgsiujvkwlx

#11: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 58832.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00401, cytochrome-c oxidase
#12: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 28585.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00410, cytochrome-c oxidase
#13: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 30383.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00420, cytochrome-c oxidase
#14: Protein Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase polypeptide IV


Mass: 17164.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Subunit contains a FLAG tag. / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P04037
#15: Protein Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 17161.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00424
#16: Protein Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase polypeptide VI


Mass: 17366.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00427
#17: Protein Cytochrome c oxidase subunit 7, mitochondrial / Cytochrome c oxidase polypeptide VII


Mass: 6942.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P10174
#18: Protein Cytochrome c oxidase subunit 9, mitochondrial / Cytochrome c oxidase polypeptide VIIA


Mass: 6974.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07255
#19: Protein Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase polypeptide VIb


Mass: 9799.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q01519
#20: Protein Cytochrome c oxidase subunit 13, mitochondrial / Cytochrome c oxidase polypeptide VIa


Mass: 15046.146 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32799
#21: Protein Cytochrome c oxidase subunit 26, mitochondrial


Mass: 7461.718 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q2V2P9

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Non-polymers , 19 types, 67 molecules

#22: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#23: Chemical ChemComp-6PH / (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate / PHOSPHATIDIC ACID


Mass: 592.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61O8P
#24: Chemical ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 691.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#25: Chemical ChemComp-CN5 / (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate / CARDIOLIPIN


Mass: 634.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H52O13P2
#26: Chemical
ChemComp-UQ6 / 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL


Mass: 592.891 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H60O4
#27: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#28: Chemical ChemComp-9PE / (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 593.773 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H60NO8P / Comment: phospholipid*YM
#29: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#30: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#31: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#32: Chemical
ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H80NO8P
#33: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#34: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#35: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#36: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#37: Chemical ChemComp-CN3 / (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate / CARDIOLIPIN


Mass: 834.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H68O17P2
#38: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#40: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Tethered supercomplexCOMPLEX#1-#210MULTIPLE SOURCES
2Ubiquinol-cytochrome c oxidoreductaseCOMPLEX#1-#101NATURAL
3Cytochrome c oxidaseCOMPLEX#11-#211NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Saccharomyces cerevisiae W303 (yeast)580240W303
32Saccharomyces cerevisiae W303 (yeast)580240W303
43Saccharomyces cerevisiae W303 (yeast)580240W303
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris-HCl pH 7.5C4H11NO31
2150 mMSodium chlorideNaCl1
31 mMPhenylmethylsulfonyl fluoride (PMSF)C7H7FO2S1
41 mMEthylenediaminetetraacetic acid (EDTA)C10H16N2O81
50.1 %DigitoninC56H92O291
6150 ng/uL3X FLAG peptideC120H169N31O49S1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: The grid is covered with a 3 nm ultrathin carbon film
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: 3 uL of sample, 5 s blot time, 30 s hold time, 0 blot force.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.6 sec. / Electron dose: 55.452 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12211
Details: Images were collected as movies composed of 40 frames.
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2particle selection
4cryoSPARC4.2CTF correction
7PHENIX1.21model fitting
9Coot0.9.8.7model refinement
10cryoSPARC4.2initial Euler assignment
11cryoSPARC4.2final Euler assignment
12cryoSPARC4.2classification
13cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1646359
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47746 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6YMX

6ymx


Accession code: 6YMX / Source name: PDB / Type: experimental model

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