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- PDB-6giq: Saccharomyces cerevisiae respiratory supercomplex III2IV -

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Entry
Database: PDB / ID: 6giq
TitleSaccharomyces cerevisiae respiratory supercomplex III2IV
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • (Cytochrome c oxidase polypeptide ...) x 2
  • (Cytochrome c oxidase subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • Unknown Cox subunit
KeywordsELECTRON TRANSPORT / Respiratory chain / supercomplex / bc1 complex / cytochrome c oxidase
Function / homology
Function and homology information


mitochondrial crista / mitochondrial respiratory chain complex IV assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial processing peptidase complex / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / mitochondrial respirasome assembly / oxidoreduction-driven active transmembrane transporter activity / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase ...mitochondrial crista / mitochondrial respiratory chain complex IV assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial processing peptidase complex / electron transporter, transferring electrons within CoQH2-cytochrome c reductase complex activity / mitochondrial respirasome assembly / oxidoreduction-driven active transmembrane transporter activity / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial respirasome / oxidative phosphorylation / integral component of mitochondrial inner membrane / electron transport coupled proton transport / ubiquinol-cytochrome-c reductase activity / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / electron transport chain / ATP synthesis coupled electron transport / mitochondrial ATP synthesis coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / chloroplast thylakoid membrane / enzyme regulator activity / aerobic respiration / nuclear periphery / 2 iron, 2 sulfur cluster binding / catalytic activity / mitochondrial intermembrane space / metalloendopeptidase activity / mitochondrial inner membrane / copper ion binding / electron transfer activity / heme binding / mitochondrion / zinc ion binding / integral component of membrane / plasma membrane / metal ion binding / cytosol
Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit III, 4-helical bundle / Peptidase M16, N-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cupredoxin / Cytochrome b-c1 complex subunit 9 ...Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit III, 4-helical bundle / Peptidase M16, N-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cupredoxin / Cytochrome b-c1 complex subunit 9 / Peptidase M16, C-terminal / Rieske iron-sulphur protein, C-terminal / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome b/b6, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit Va/VI / Rieske iron-sulphur protein / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome b / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit I domain / Cytochrome b/b6-like domain superfamily / Di-haem cytochrome, transmembrane / Cytochrome c oxidase subunit III / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome b-c1 complex subunit 10, fungi / Cytochrome c oxidase, subunit VIa, conserved site / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 7 / Cytochrome c1 / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome C oxidase subunit II, periplasmic domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge protein / Ubiquinol-cytochrome C reductase complex 14kD subunit / UcrQ family / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C1 family / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VIIc / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit Vb / Rieske [2Fe-2S] domain / Cytochrome b/b6/petB / Cytochrome c-like domain superfamily / Copper centre Cu(A) / Peptidase M16, zinc-binding site / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase subunit I / Cytochrome c oxidase subunit III-like / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b(C-terminal)/b6/petD / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase subunit VII / Insulinase (Peptidase family M16) / Peptidase M16 inactive domain / Cytochrome c oxidase, subunit VIb superfamily / Ubiquinol cytochrome reductase, transmembrane domain / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain F / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal
Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 7A / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit 6A, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 6B / Cytochrome b-c1 complex subunit 1, mitochondrial ...Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 7A / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit 6A, mitochondrial / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 6B / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c oxidase polypeptide VIII, mitochondrial / Cytochrome c oxidase subunit 4, mitochondrial / Cytochrome c oxidase subunit 6, mitochondrial / Cytochrome c oxidase polypeptide 5A, mitochondrial / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 1 / Cytochrome b / Cytochrome b-c1 complex subunit 7
Biological speciesSaccharomyces cerevisiae W303 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsRathore, S. / Berndtsson, J. / Conrad, J. / Ott, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Cryo-EM structure of the yeast respiratory supercomplex.
Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott /
Abstract: Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes ...Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes IIIIV and IIIIV, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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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
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Cytochrome b-c1 complex subunit 9
L: Cytochrome b-c1 complex subunit 1, mitochondrial
M: Cytochrome b-c1 complex subunit 2, mitochondrial
N: Cytochrome b
O: Cytochrome c1, heme protein, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: Cytochrome b-c1 complex subunit 6
R: Cytochrome b-c1 complex subunit 7
S: Cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 9
U: Cytochrome b-c1 complex subunit 10
V: Cytochrome b-c1 complex subunit 10
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 polypeptide 5A, mitochondrial
f: Cytochrome c oxidase subunit 6, mitochondrial
g: Cytochrome c oxidase subunit 7
h: Cytochrome c oxidase polypeptide VIII, mitochondrial
i: Cytochrome c oxidase subunit 7A
j: Cytochrome c oxidase subunit 6B
k: Cytochrome c oxidase subunit 6A, mitochondrial
m: Unknown Cox subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)736,64058
Polymers721,68332
Non-polymers14,95726
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Other experiment performed that support the state of this assembly is native gel electrophoresis and co-purification combined with determination of enzyme quantity.
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area128830 Å2
ΔGint-1044 kcal/mol
Surface area224990 Å2
MethodPISA

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Components

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

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


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 reductase complex 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 reductase iron- ...Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase 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 / 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 reductase complex 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 / Complex III subunit 7 / Complex III subunit VII / Ubiquinol-cytochrome c reductase c reductase ...Complex III subunit 7 / Complex III subunit VII / Ubiquinol-cytochrome c reductase c reductase complex 14 kDa protein


Mass: 14583.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00128
#8: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VII / Ubiquinol-cytochrome c reductase complex 11 kDa ...Complex III subunit 8 / Complex III subunit VII / Ubiquinol-cytochrome c reductase complex 11 kDa protein / Ubiquinol-cytochrome c reductase complex 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 / 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 reductase complex 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 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 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 CNDO

#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 reductase 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
#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 reductase complex 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

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Cytochrome c oxidase subunit ... , 9 types, 9 molecules abcdfgijk

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


Mass: 58832.586 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P04037, cytochrome-c oxidase
#16: Protein Cytochrome c oxidase subunit 6, mitochondrial / / Cytochrome c oxidase polypeptide VI


Mass: 17366.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00427, cytochrome-c oxidase
#17: Protein Cytochrome c oxidase subunit 7 / / Cytochrome c oxidase polypeptide VII


Mass: 6942.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P10174, cytochrome-c oxidase
#19: Protein Cytochrome c oxidase subunit 7A / / Cytochrome c oxidase polypeptide VIIA


Mass: 6974.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07255, cytochrome-c oxidase
#20: Protein Cytochrome c oxidase subunit 6B / / Cytochrome c oxidase polypeptide VIb


Mass: 9799.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q01519, cytochrome-c oxidase
#21: Protein Cytochrome c oxidase subunit 6A, mitochondrial / / Cytochrome c oxidase polypeptide VIa


Mass: 15046.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32799, cytochrome-c oxidase

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Cytochrome c oxidase polypeptide ... , 2 types, 2 molecules eh

#15: Protein Cytochrome c oxidase polypeptide 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 17161.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00424, cytochrome-c oxidase
#18: Protein Cytochrome c oxidase polypeptide VIII, mitochondrial


Mass: 8921.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P04039, cytochrome-c oxidase

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Protein/peptide , 1 types, 1 molecules m

#22: Protein/peptide Unknown Cox subunit


Mass: 2656.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae W303 (yeast)

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Non-polymers , 13 types, 26 molecules

#23: Chemical ChemComp-6PH / (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 592.785 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61O8P
#24: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#25: 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
#26: 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 / Cardiolipin


Mass: 634.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H52O13P2
#27: 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.: 2 / Source method: obtained synthetically / Formula: C39H60O4
#28: Chemical ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 564.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H57O8P
#29: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P
#31: 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
#32: 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 / Cardiolipin


Mass: 834.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H68O17P2
#33: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#34: Chemical ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#35: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2

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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
1Saccharomyces cerevisiae Supercomplex (III2IV)COMPLEX1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,220NATURAL
2Saccharomyces cerevisiae complex IIICOMPLEX1,2,3,4,5,6,7,8,9,101NATURAL
3Saccharomyces cerevisiae complex IVCOMPLEX11,12,13,14,15,16,17,18,19,20,21,221NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDOrganelle
21Saccharomyces cerevisiae W303 (yeast)580240Mitochondria
32Saccharomyces cerevisiae W303 (yeast)580240Mitochondria
43Saccharomyces cerevisiae W303 (yeast)580240Mitochondria
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
9PHENIX1.13model refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203271 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-Correlation coefficient

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