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- PDB-6ymx: CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 6ymx
TitleCIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae
Components
  • (Cytochrome b-c1 complex subunit ...) x 11
  • (Cytochrome c oxidase subunit ...) x 12
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsELECTRON TRANSPORT / Complex / CIII / CIV / Supercomplex
Function / homology
Function and homology information


mitochondrial cytochrome c oxidase assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respirasome assembly / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase ...mitochondrial cytochrome c oxidase assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respirasome assembly / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / mitochondrial respirasome / cytochrome-c oxidase / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / proton transmembrane transport / nuclear periphery / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / 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 VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily ...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 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 VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / 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 I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / 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 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 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 b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome c oxidase subunit III-like superfamily / 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 oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b / : / : / Cytochrome c/quinol oxidase subunit II / 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. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / 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. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Di-haem cytochrome, transmembrane / Cytochrome C oxidase subunit II, periplasmic domain / Rieske iron-sulphur protein / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
Chem-6PH / Chem-7PH / Chem-8PE / Chem-9PE / Chem-CN3 / Chem-CN5 / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A ...Chem-6PH / Chem-7PH / Chem-8PE / Chem-9PE / Chem-CN3 / Chem-CN5 / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / 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 (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsBerndtsson, J. / Rathore, S. / Ott, M.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2014-4116 Sweden
Swedish Research Council2018-03694 Sweden
Knut and Alice Wallenberg Foundation2017.0091 Sweden
Knut and Alice Wallenberg Foundation2013.0006 Sweden
CitationJournal: EMBO Rep / Year: 2020
Title: Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance.
Authors: Jens Berndtsson / Andreas Kohler / Sorbhi Rathore / Lorena Marin-Buera / Hannah Dawitz / Jutta Diessl / Verena Kohler / Antoni Barrientos / Sabrina Büttner / Flavia Fontanesi / Martin Ott /
Abstract: Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in ...Respiratory chains are crucial for cellular energy conversion and consist of multi-subunit complexes that can assemble into supercomplexes. These structures have been intensively characterized in various organisms, but their physiological roles remain unclear. Here, we elucidate their function by leveraging a high-resolution structural model of yeast respiratory supercomplexes that allowed us to inhibit supercomplex formation by mutation of key residues in the interaction interface. Analyses of a mutant defective in supercomplex formation, which still contains fully functional individual complexes, show that the lack of supercomplex assembly delays the diffusion of cytochrome c between the separated complexes, thus reducing electron transfer efficiency. Consequently, competitive cellular fitness is severely reduced in the absence of supercomplex formation and can be restored by overexpression of cytochrome c. In sum, our results establish how respiratory supercomplexes increase the efficiency of cellular energy conversion, thereby providing an evolutionary advantage for aerobic organisms.
History
DepositionApr 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
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
h: Cytochrome c oxidase subunit 8, mitochondrial
i: Cytochrome c oxidase subunit 9, mitochondrial
j: Cytochrome c oxidase subunit 12, mitochondrial
k: Cytochrome c oxidase subunit 13, mitochondrial
m: Cytochrome c oxidase subunit 26, mitochondrial
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
H: Cytochrome b-c1 complex subunit 8, mitochondrial
I: Cytochrome b-c1 complex subunit 9, mitochondrial
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, mitochondrial
R: Cytochrome b-c1 complex subunit 7, mitochondrial
S: Cytochrome b-c1 complex subunit 8, mitochondrial
T: Cytochrome b-c1 complex subunit 9, mitochondrial
U: Cytochrome b-c1 complex subunit 10, mitochondrial
V: Cytochrome b-c1 complex subunit 10, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)669,78770
Polymers646,59032
Non-polymers23,19738
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area161880 Å2
ΔGint-1265 kcal/mol
Surface area217880 Å2
MethodPISA

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Components

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Cytochrome c oxidase subunit ... , 12 types, 12 molecules abcdefghijkm

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


Mass: 58316.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00401, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 26779.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00410, cytochrome-c oxidase
#3: Protein Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


Mass: 30252.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00420, cytochrome-c oxidase
#4: Protein Cytochrome c oxidase subunit 4, mitochondrial / / Cytochrome c oxidase polypeptide IV


Mass: 12694.382 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04037
#5: Protein Cytochrome c oxidase subunit 5A, mitochondrial / / Cytochrome c oxidase polypeptide Va


Mass: 14324.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00424
#6: Protein Cytochrome c oxidase subunit 6, mitochondrial / / Cytochrome c oxidase polypeptide VI


Mass: 11725.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00427
#7: Protein Cytochrome c oxidase subunit 7, mitochondrial / / Cytochrome c oxidase polypeptide VII


Mass: 6410.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P10174
#8: Protein Cytochrome c oxidase subunit 8, mitochondrial / / Cytochrome c oxidase polypeptide VIII


Mass: 5737.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P04039
#9: Protein Cytochrome c oxidase subunit 9, mitochondrial / / Cytochrome c oxidase polypeptide VIIA


Mass: 6241.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P07255
#10: Protein Cytochrome c oxidase subunit 12, mitochondrial / / Cytochrome c oxidase polypeptide VIb


Mass: 9225.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q01519
#11: Protein Cytochrome c oxidase subunit 13, mitochondrial / / Cytochrome c oxidase polypeptide VIa


Mass: 13306.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32799
#12: Protein/peptide Cytochrome c oxidase subunit 26, mitochondrial /


Mass: 4347.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q2V2P9

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Cytochrome b-c1 complex subunit ... , 11 types, 16 molecules ALBMEPFGRHSIQTUV

#13: 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: 47459.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P07256
#14: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome c oxidoreductase core protein 2


Mass: 38751.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P07257
#17: 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: 20122.955 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P08067, quinol-cytochrome-c reductase
#18: 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: 8854.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00127
#19: Protein Cytochrome b-c1 complex subunit 7, 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


Mass: 14452.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00128
#20: 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: 10856.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P08525
#21: 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: 6214.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22289
#22: 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: 8983.905 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00127
#23: 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: 6230.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22289
#24: Protein/peptide 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: 4920.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P37299
#25: 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: 5750.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P37299

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Protein , 2 types, 4 molecules CNDO

#15: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P00163, quinol-cytochrome-c reductase
#16: 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: 27807.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P07143, quinol-cytochrome-c reductase

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Non-polymers , 15 types, 38 molecules

#26: Chemical ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#29: 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.: 2 / Source method: obtained synthetically / Formula: C36H68O17P2
#30: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#31: Chemical
ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Dipalmitoylphosphatidylcholine


Mass: 734.039 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION
#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#33: 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
#34: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#40: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

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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: Respiratroy supercopmlex CIII2/CIV / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: W303-1b / Organelle: Mitochondria
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTrisC4H11NO31
2150 mMSodium chlorideNaClSodium chloride1
30.1 %DigitoninC56H92O291
41 mMphenylmethylsulfonyl fluoridePMSFC7H7FO2S1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 / Nominal magnification: 130000 X / Nominal defocus max: -3 nm / Nominal defocus min: -1.4 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8775
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1RELION2particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
10cryoSPARC2initial Euler assignment
11cryoSPARC2final Euler assignment
12cryoSPARC2classification
13cryoSPARC23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 647805
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201223 / Num. of class averages: 1 / Symmetry type: POINT

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