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- PDB-6t15: The III2-IV(5B)1 respiratory supercomplex from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 6t15
TitleThe III2-IV(5B)1 respiratory supercomplex from S. cerevisiae
Components
  • (CYTOCHROME B-C1 COMPLEX SUBUNIT ...) x 9
  • (CYTOCHROME C OXIDASE SUBUNIT ...) x 9
  • (Cytochrome c oxidase ...) x 2
  • COX26; SYNONYM: Uncharacterized protein YDR119W-A
  • CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL; SYNONYM: 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
  • RCF2; SYNONYM: Respiratory supercomplex factor 2
KeywordsOXIDOREDUCTASE / CYTOCHROME C OXIDASE CYTOCHROME BC1 MITOCHONDRIA RESPIRATORY CHAIN SUPERCOMPLEX / ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
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 respiratory chain complex III assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : ...: / 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 respiratory chain complex III assembly / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / : / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / nuclear periphery / proton transmembrane transport / mitochondrial membrane / positive regulation of protein-containing complex assembly / 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 / membrane / metal ion binding / cytosol
Similarity search - Function
Respiratory supercomplex factor 2, mitochondrial / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 ...Respiratory supercomplex factor 2, mitochondrial / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit III, four-helix bundle / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c 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 VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / 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 III domain / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / 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 b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / 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 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / 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 / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c/quinol oxidase subunit II / : / 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 b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily
Similarity search - Domain/homology
CARDIOLIPIN / 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 / Cytochrome b-c1 complex subunit 6, mitochondrial ...CARDIOLIPIN / 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 / 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 5B, 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 / Respiratory supercomplex factor 2, mitochondrial / Cytochrome c oxidase subunit 12, mitochondrial / Cytochrome c oxidase subunit 26, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsMarechal, A. / Pinotsis, N. / Hartley, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M00936X/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes.
Authors: Andrew M Hartley / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal /
Abstract: The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, ...The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, remain to be determined. In , cytochrome oxidase (CIV) forms SCs of varying stoichiometry with cytochrome (CIII). Recent studies have revealed, in normoxic growth conditions, an interface made exclusively by Cox5A, the only yeast respiratory protein that exists as one of two isoforms depending on oxygen levels. Here we present the cryo-EM structures of the III-IV and III-IV SCs containing the hypoxic isoform Cox5B solved at 3.4 and 2.8 Å, respectively. We show that the change of isoform does not affect SC formation or activity, and that SC stoichiometry is dictated by the level of CIII/CIV biosynthesis. Comparison of the CIV- and CIV-containing SC structures highlighted few differences, found mainly in the region of Cox5. Additional density was revealed in all SCs, independent of the CIV isoform, in a pocket formed by Cox1, Cox3, Cox12, and Cox13, away from the CIII-CIV interface. In the CIV-containing hypoxic SCs, this could be confidently assigned to the hypoxia-induced gene 1 (Hig1) type 2 protein Rcf2. With conserved residues in mammalian Hig1 proteins and Cox3/Cox12/Cox13 orthologs, we propose that Hig1 type 2 proteins are stoichiometric subunits of CIV, at least when within a III-IV SC.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Assembly

Deposited unit
A: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 1, CORE PROTEIN I, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 1
B: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
C: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C COMPLEX CORE PROTEIN 2
D: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL; SYNONYM: 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
E: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 5, RIESKE IRON-SULFUR PROTEIN, RISP, UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
F: CYTOCHROME B-C1 COMPLEX SUBUNIT 6; SYNONYM: 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
G: CYTOCHROME B-C1 COMPLEX SUBUNIT 7; SYNONYM: COMPLEX III SUBUNIT 7,COMPLEX III SUBUNIT VII,UBIQUINOL-CYTOCHROME C REDUCTASE C REDUCTASE COMPLEX 14 KDA PROTEIN
H: CYTOCHROME B-C1 COMPLEX SUBUNIT 8; SYNONYM: 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
I: CYTOCHROME B-C1 COMPLEX SUBUNIT 9; SYNONYM: 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
J: CYTOCHROME B-C1 COMPLEX SUBUNIT 10; SYNONYM: COMPLEX III SUBUNIT 10,COMPLEX III SUBUNIT XI, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 8.5 KDA PROTEIN
L: CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 1, CORE PROTEIN I, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 1
M: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
N: CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C COMPLEX CORE PROTEIN 2
O: CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL; SYNONYM: 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
P: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 5, RIESKE IRON-SULFUR PROTEIN, RISP, UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT
Q: CYTOCHROME B-C1 COMPLEX SUBUNIT 6; SYNONYM: 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
R: CYTOCHROME B-C1 COMPLEX SUBUNIT 7; SYNONYM: COMPLEX III SUBUNIT 7,COMPLEX III SUBUNIT VII,UBIQUINOL-CYTOCHROME C REDUCTASE C REDUCTASE COMPLEX 14 KDA PROTEIN
S: CYTOCHROME B-C1 COMPLEX SUBUNIT 8; SYNONYM: 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
T: CYTOCHROME B-C1 COMPLEX SUBUNIT 9; SYNONYM: 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
U: CYTOCHROME B-C1 COMPLEX SUBUNIT 10; SYNONYM: COMPLEX III SUBUNIT 10,COMPLEX III SUBUNIT XI, UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 8.5 KDA PROTEIN
a: CYTOCHROME C OXIDASE SUBUNIT 1; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE I, COX1
b: CYTOCHROME C OXIDASE SUBUNIT 2; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE II, COX2
c: CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3
d: CYTOCHROME C OXIDASE SUBUNIT 4, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE IV, COX4
e: CYTOCHROME C OXIDASE POLYPEPTIDE 5B, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VB, COX5B
f: CYTOCHROME C OXIDASE SUBUNIT 6, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VI, COX6
g: CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7
h: Cytochrome c oxidase polypeptide VIII, mitochondrial
i: CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9
j: Cytochrome c oxidase subunit 6B
k: CYTOCHROME C OXIDASE SUBUNIT 6A, MITOCHONDRIAL; CYTOCHROME C OXIDASE POLYPEPTIDE VIA, COX13
l: COX26; SYNONYM: Uncharacterized protein YDR119W-A
m: RCF2; SYNONYM: Respiratory supercomplex factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)741,47778
Polymers708,32933
Non-polymers33,14845
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area187880 Å2
ΔGint-1565 kcal/mol
Surface area225930 Å2
MethodPISA

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Components

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CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 9 types, 18 molecules ALBMCNEPFQGRHSITJU

#1: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 1, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 1, CORE PROTEIN I, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 1


Mass: 47459.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07256
#2: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 38751.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07257
#3: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 2, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 2, CORE PROTEIN II, UBIQUINOL-CYTOCHROME-C COMPLEX CORE PROTEIN 2


Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00163
#5: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL; SYNONYM: COMPLEX III SUBUNIT 5, RIESKE IRON-SULFUR PROTEIN, RISP, UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT


Mass: 20122.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase
#6: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 6; SYNONYM: 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 S288C (yeast) / References: UniProt: P00127
#7: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 7; SYNONYM: 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 S288C (yeast) / References: UniProt: P00128
#8: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 8; SYNONYM: 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 S288C (yeast) / References: UniProt: P08525
#9: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 9; SYNONYM: 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 S288C (yeast) / References: UniProt: P22289
#10: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 10; SYNONYM: 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 S288C (yeast) / References: UniProt: P37299

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Protein , 3 types, 4 molecules DOlm

#4: Protein CYTOCHROME C1, HEME PROTEIN, MITOCHONDRIAL; SYNONYM: 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: 27807.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07143
#22: Protein COX26; SYNONYM: Uncharacterized protein YDR119W-A


Mass: 7461.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q2V2P9
#23: Protein RCF2; SYNONYM: Respiratory supercomplex factor 2


Mass: 25381.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P53721

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CYTOCHROME C OXIDASE SUBUNIT ... , 9 types, 9 molecules abcdfgijk

#11: Protein CYTOCHROME C OXIDASE SUBUNIT 1; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE I, COX1


Mass: 58832.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00401, cytochrome-c oxidase
#12: Protein CYTOCHROME C OXIDASE SUBUNIT 2; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE II, COX2


Mass: 26779.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00410, cytochrome-c oxidase
#13: Protein CYTOCHROME C OXIDASE SUBUNIT 3; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE III, COX3


Mass: 30383.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00420, cytochrome-c oxidase
#14: Protein CYTOCHROME C OXIDASE SUBUNIT 4, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE IV, COX4


Mass: 14188.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04037, cytochrome-c oxidase
#16: Protein CYTOCHROME C OXIDASE SUBUNIT 6, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VI, COX6


Mass: 12641.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00427, cytochrome-c oxidase
#17: Protein CYTOCHROME C OXIDASE SUBUNIT 7; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VII, COX7


Mass: 6811.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P10174, cytochrome-c oxidase
#19: Protein CYTOCHROME C OXIDASE SUBUNIT 7A; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIIA, COX9


Mass: 6471.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P07255, cytochrome-c oxidase
#20: Protein Cytochrome c oxidase subunit 6B / Cytochrome c oxidase polypeptide VIb


Mass: 9668.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q01519, cytochrome-c oxidase
#21: Protein CYTOCHROME C OXIDASE SUBUNIT 6A, MITOCHONDRIAL; CYTOCHROME C OXIDASE POLYPEPTIDE VIA, COX13


Mass: 15117.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: COX13, YGL191W, G1341 / Production host: Saccharomyces cerevisiae S288C (yeast) / Variant (production host): W303-1B / References: UniProt: P32799, cytochrome-c oxidase

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

#15: Protein CYTOCHROME C OXIDASE POLYPEPTIDE 5B, MITOCHONDRIAL; SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VB, COX5B


Mass: 15325.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P00425, cytochrome-c oxidase
#18: Protein Cytochrome c oxidase polypeptide VIII, mitochondrial


Mass: 5737.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P04039, cytochrome-c oxidase

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Non-polymers , 11 types, 45 molecules

#24: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#25: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#26: 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.: 7 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#27: Chemical
ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H80NO8P
#28: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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

ComponentName: The III2-IV(5B)1 respiratory supercomplex from S. cerevisiae
Type: COMPLEX
Details: A Delta-cox5a Delta-rox1 strain used for this complex that only expresses Cox5B
Entity ID: #1-#23 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: 3 microliter of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 s

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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 FIELD
Image recordingElectron dose: 56.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2EPU2.3image acquisition
4cryoSPARC2CTF correction
7UCSF Chimera1.13.1model fitting
9cryoSPARC2initial Euler assignment
10cryoSPARC2final Euler assignment
11cryoSPARC2classification
12cryoSPARC23D reconstruction
13PHENIX1.14-3260model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73042 / Symmetry type: POINT
Atomic model buildingB value: 80 / Protocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6HU9

6hu9

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