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- PDB-8e7s: III2IV2 respiratory supercomplex from Saccharomyces cerevisiae wi... -

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Entry
Database: PDB / ID: 8e7s
TitleIII2IV2 respiratory supercomplex from Saccharomyces cerevisiae with 4 bound UQ6
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • (Cytochrome c oxidase subunit ...) x 12
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / S.cerevisiae / respiratory supercomplex / cardiolipin / UQ6
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 / cytochrome-c oxidase activity / electron transport coupled proton transport / 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. / 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 / Peptidase M16, zinc-binding site / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Insulinase family, zinc-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
CARDIOLIPIN / 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 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-UQ6 ...CARDIOLIPIN / 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 / DI-PALMITOYL-3-SN-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: 3.2 Å
AuthorsHryc, C.F. / Mileykovskaya, E. / Baker, M. / Dowhan, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115969 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM063210 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex.
Authors: Corey F Hryc / Venkata K P S Mallampalli / Evgeniy I Bovshik / Stavros Azinas / Guizhen Fan / Irina I Serysheva / Genevieve C Sparagna / Matthew L Baker / Eugenia Mileykovskaya / William Dowhan /
Abstract: Cardiolipin is a hallmark phospholipid of mitochondrial membranes. Despite established significance of cardiolipin in supporting respiratory supercomplex organization, a mechanistic understanding of ...Cardiolipin is a hallmark phospholipid of mitochondrial membranes. Despite established significance of cardiolipin in supporting respiratory supercomplex organization, a mechanistic understanding of this lipid-protein interaction is still lacking. To address the essential role of cardiolipin in supercomplex organization, we report cryo-EM structures of a wild type supercomplex (IVIIIIV) and a supercomplex (IIIIV) isolated from a cardiolipin-lacking Saccharomyces cerevisiae mutant at 3.2-Å and 3.3-Å resolution, respectively, and demonstrate that phosphatidylglycerol in IIIIV occupies similar positions as cardiolipin in IVIIIIV. Lipid-protein interactions within these complexes differ, which conceivably underlies the reduced level of IVIIIIV and high levels of IIIIV and free III and IV in mutant mitochondria. Here we show that anionic phospholipids interact with positive amino acids and appear to nucleate a phospholipid domain at the interface between the individual complexes, which dampen charge repulsion and further stabilize interaction, respectively, between individual complexes.
History
DepositionAug 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: 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-c1 complex subunit Rieske, mitochondrial
D: Cytochrome b-c1 complex subunit 10, mitochondrial
E: Cytochrome b-c1 complex subunit 9, mitochondrial
F: Cytochrome b-c1 complex subunit 7, mitochondrial
G: Cytochrome b-c1 complex subunit 6, mitochondrial
H: Cytochrome b-c1 complex subunit 8, mitochondrial
J: Cytochrome b
K: Cytochrome c oxidase subunit 1
L: Cytochrome c1, heme protein, mitochondrial
M: Cytochrome c oxidase subunit 8, mitochondrial
N: Cytochrome c oxidase subunit 7, mitochondrial
O: Cytochrome c oxidase subunit 3
P: Cytochrome c oxidase subunit 2
Q: Cytochrome c oxidase subunit 6, mitochondrial
R: Cytochrome c oxidase subunit 9, mitochondrial
S: Cytochrome c oxidase subunit 13, mitochondrial
T: Cytochrome c oxidase subunit 4, mitochondrial
U: Cytochrome c oxidase subunit 12, mitochondrial
V: Cytochrome c oxidase subunit 26, mitochondrial
W: Cytochrome c oxidase subunit 5A, mitochondrial
a: Cytochrome b-c1 complex subunit 1, mitochondrial
b: Cytochrome b-c1 complex subunit 2, mitochondrial
c: Cytochrome b-c1 complex subunit Rieske, mitochondrial
d: Cytochrome b-c1 complex subunit 10, mitochondrial
e: Cytochrome b-c1 complex subunit 9, mitochondrial
f: Cytochrome b-c1 complex subunit 7, mitochondrial
g: Cytochrome b-c1 complex subunit 6, mitochondrial
h: Cytochrome b-c1 complex subunit 8, mitochondrial
j: Cytochrome b
k: Cytochrome c oxidase subunit 1
l: Cytochrome c1, heme protein, mitochondrial
m: Cytochrome c oxidase subunit 8, mitochondrial
n: Cytochrome c oxidase subunit 7, mitochondrial
o: Cytochrome c oxidase subunit 3
p: Cytochrome c oxidase subunit 2
q: Cytochrome c oxidase subunit 6, mitochondrial
r: Cytochrome c oxidase subunit 9, mitochondrial
s: Cytochrome c oxidase subunit 13, mitochondrial
t: Cytochrome c oxidase subunit 4, mitochondrial
u: Cytochrome c oxidase subunit 12, mitochondrial
v: Cytochrome c oxidase subunit 26, mitochondrial
w: Cytochrome c oxidase subunit 5A, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)997,884107
Polymers951,12844
Non-polymers46,75563
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#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 (brewer's yeast) / Strain: ATCC 204508 / S288c / 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 (brewer's yeast) / References: UniProt: P07257
#3: 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 (brewer's yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase
#4: 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 (brewer's yeast) / References: UniProt: P37299
#5: 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 (brewer's yeast) / References: UniProt: P22289
#6: 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: 14583.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00128
#7: 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 (brewer's yeast) / References: UniProt: P00127
#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 (brewer's yeast) / References: UniProt: P08525

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Protein , 2 types, 4 molecules JjLl

#9: 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 (brewer's yeast) / References: UniProt: P00163, quinol-cytochrome-c reductase
#11: 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 (brewer's yeast) / References: UniProt: P07143, quinol-cytochrome-c reductase

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Cytochrome c oxidase subunit ... , 12 types, 24 molecules KkMmNnOoPpQqRrSsTtUuVvWw

#10: 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 (brewer's yeast) / References: UniProt: P00401, cytochrome-c oxidase
#12: Protein Cytochrome c oxidase subunit 8, mitochondrial / / Cytochrome c oxidase polypeptide VIII


Mass: 8921.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04039
#13: 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 (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P10174
#14: 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 (brewer's yeast) / References: UniProt: P00420, cytochrome-c oxidase
#15: 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 (brewer's yeast) / References: UniProt: P00410, cytochrome-c oxidase
#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 (brewer's yeast) / References: UniProt: P00427
#17: 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 (brewer's yeast) / References: UniProt: P07255
#18: 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 (brewer's yeast) / References: UniProt: P32799
#19: 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04037
#20: 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 (brewer's yeast) / References: UniProt: Q01519
#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 (brewer's yeast) / References: UniProt: Q2V2P9
#22: 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 (brewer's yeast) / References: UniProt: P00424

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Non-polymers , 10 types, 63 molecules

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


Mass: 691.959 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C37H74NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#24: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#25: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#26: Chemical
ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Dipalmitoylphosphatidylcholine


Mass: 734.039 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION
#27: 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
#28: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#29: 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 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical
ChemComp-HEA / HEME-A / Heme A


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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#32: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu2

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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: III2-IV2 mitochondrial respiratory supercomplex / Type: COMPLEX / Entity ID: #1-#22 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY00b
Buffer solutionpH: 7.2
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 / Nominal magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 20253
Image scansWidth: 360 / Height: 360 / Movie frames/image: 35 / Used frames/image: 1-35

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
EM software
IDNameCategory
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1510025
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 493055 / Symmetry type: POINT

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