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- EMDB-27940: III2IV2 respiratory supercomplex from Saccharomyces cerevisiae wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-27940
TitleIII2IV2 respiratory supercomplex from Saccharomyces cerevisiae with 4 bound UQ6
Map dataFinal Density Map
Sample
  • Complex: III2-IV2 mitochondrial respiratory supercomplex
    • Protein or peptide: x 22 types
  • Ligand: x 10 types
KeywordsS.cerevisiae / respiratory supercomplex / cardiolipin / UQ6 / OXIDOREDUCTASE
Function / homology
Function and homology information


Complex III assembly / : / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV ...Complex III assembly / : / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial cytochrome c oxidase assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV / cellular respiration / respiratory chain complex / cytochrome-c oxidase / respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / ubiquinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / nuclear periphery / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / membrane / cytosol
Similarity search - Function
Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb ...Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile.
Similarity search - Domain/homology
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 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHryc CF / Mileykovskaya E / Baker M / Dowhan W
Funding support United States, 2 items
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, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27940.png

Downloads & links

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Map

FileDownload / File: emd_27940.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal Density Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.245
Minimum - Maximum-0.87319577 - 1.8436114
Average (Standard dev.)0.00798144 (±0.053222314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_27940_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_27940_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : III2-IV2 mitochondrial respiratory supercomplex

EntireName: III2-IV2 mitochondrial respiratory supercomplex
Components
  • Complex: III2-IV2 mitochondrial respiratory supercomplex
    • Protein or peptide: Cytochrome b-c1 complex subunit 1, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 10, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 9, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 7, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 6, mitochondrial
    • Protein or peptide: Cytochrome b-c1 complex subunit 8, mitochondrial
    • Protein or peptide: Cytochrome b
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c1, heme protein, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 8, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 7, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 6, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 9, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 13, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 4, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 12, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 26, mitochondrial
    • Protein or peptide: Cytochrome c oxidase subunit 5A, mitochondrial
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: CARDIOLIPIN
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: 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
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: DINUCLEAR COPPER ION

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Supramolecule #1: III2-IV2 mitochondrial respiratory supercomplex

SupramoleculeName: III2-IV2 mitochondrial respiratory supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY00b

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Macromolecule #1: Cytochrome b-c1 complex subunit 1, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 1, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 50.282594 KDa
SequenceString: MLRTVTSKTV SNQFKRSLAT AVATPKAEVT QLSNGIVVAT EHNPSAHTAS VGVVFGSGAA NENPYNNGVS NLWKNIFLSK ENSAVAAKE GLALSSNISR DFQSYIVSSL PGSTDKSLDF LNQSFIQQKA NLLSSSNFEA TKKSVLKQVQ DFEENDHPNR V LEHLHSTA ...String:
MLRTVTSKTV SNQFKRSLAT AVATPKAEVT QLSNGIVVAT EHNPSAHTAS VGVVFGSGAA NENPYNNGVS NLWKNIFLSK ENSAVAAKE GLALSSNISR DFQSYIVSSL PGSTDKSLDF LNQSFIQQKA NLLSSSNFEA TKKSVLKQVQ DFEENDHPNR V LEHLHSTA FQNTPLSLPT RGTLESLENL VVADLESFAN NHFLNSNAVV VGTGNIKHED LVNSIESKNL SLQTGTKPVL KK KAAFLGS EVRLRDDTLP KAWISLAVEG EPVNSPNYFV AKLAAQIFGS YNAFEPASRL QGIKLLDNIQ EYQLCDNFNH FSL SYKDSG LWGFSTATRN VTMIDDLIHF TLKQWNRLTI SVTDTEVERA KSLLKLQLGQ LYESGNPVND ANLLGAEVLI KGSK LSLGE AFKKIDAITV KDVKAWAGKR LWDQDIAIAG TGQIEGLLDY MRIRSDMSMM RW

UniProtKB: Cytochrome b-c1 complex subunit 1, mitochondrial

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Macromolecule #2: Cytochrome b-c1 complex subunit 2, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 2, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 40.528008 KDa
SequenceString: MLSAARLQFA QGSVRRLTVS ARDAPTKIST LAVKVHGGSR YATKDGVAHL LNRFNFQNTN TRSALKLVRE SELLGGTFKS TLDREYITL KATFLKDDLP YYVNALADVL YKTAFKPHEL TESVLPAARY DYAVAEQCPV KSAEDQLYAI TFRKGLGNPL L YDGVERVS ...String:
MLSAARLQFA QGSVRRLTVS ARDAPTKIST LAVKVHGGSR YATKDGVAHL LNRFNFQNTN TRSALKLVRE SELLGGTFKS TLDREYITL KATFLKDDLP YYVNALADVL YKTAFKPHEL TESVLPAARY DYAVAEQCPV KSAEDQLYAI TFRKGLGNPL L YDGVERVS LQDIKDFADK VYTKENLEVS GENVVEADLK RFVDESLLST LPAGKSLVSK SEPKFFLGEE NRVRFIGDSV AA IGIPVNK ASLAQYEVLA NYLTSALSEL SGLISSAKLD KFTDGGLFTL FVRDQDSAVV SSNIKKIVAD LKKGKDLSPA INY TKLKNA VQNESVSSPI ELNFDAVKDF KLGKFNYVAV GDVSNLPYLD EL

UniProtKB: Cytochrome b-c1 complex subunit 2, mitochondrial

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Macromolecule #3: Cytochrome b-c1 complex subunit Rieske, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 23.393973 KDa
SequenceString: MLGIRSSVKT CFKPMSLTSK RLISQSLLAS KSTYRTPNFD DVLKENNDAD KGRSYAYFMV GAMGLLSSAG AKSTVETFIS SMTATADVL AMAKVEVNLA AIPLGKNVVV KWQGKPVFIR HRTPHEIQEA NSVDMSALKD PQTDADRVKD PQWLIMLGIC T HLGCVPIG ...String:
MLGIRSSVKT CFKPMSLTSK RLISQSLLAS KSTYRTPNFD DVLKENNDAD KGRSYAYFMV GAMGLLSSAG AKSTVETFIS SMTATADVL AMAKVEVNLA AIPLGKNVVV KWQGKPVFIR HRTPHEIQEA NSVDMSALKD PQTDADRVKD PQWLIMLGIC T HLGCVPIG EAGDFGGWFC PCHGSHYDIS GRIRKGPAPL NLEIPAYEFD GDKVIVG

UniProtKB: Cytochrome b-c1 complex subunit Rieske, mitochondrial

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Macromolecule #4: Cytochrome b-c1 complex subunit 10, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 10, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.602913 KDa
SequenceString:
MAYTSHLSSK TGLHFGRLSL RSLTAYAPNL MLWGGASMLG LFVFTEGWPK FQDTLYKKIP LLGPTLEDHT PPEDKPN

UniProtKB: Cytochrome b-c1 complex subunit 10, mitochondrial

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Macromolecule #5: Cytochrome b-c1 complex subunit 9, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 9, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.485334 KDa
SequenceString:
MSFSSLYKTF FKRNAVFVGT IFAGAFVFQT VFDTAITSWY ENHNKGKLWK DVKARIAAGD GDDDDE

UniProtKB: Cytochrome b-c1 complex subunit 9, mitochondrial

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Macromolecule #6: Cytochrome b-c1 complex subunit 7, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 7, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.583755 KDa
SequenceString:
MPQSFTSIAR IGDYILKSPV LSKLCVPVAN QFINLAGYKK LGLKFDDLIA EENPIMQTAL RRLPEDESYA RAYRIIRAHQ TELTHHLLP RNEWIKAQED VPYLLPYILE AEAAAKEKDE LDNIEVSK

UniProtKB: Cytochrome b-c1 complex subunit 7, mitochondrial

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Macromolecule #7: Cytochrome b-c1 complex subunit 6, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.276074 KDa
SequenceString:
MGMLELVGEY WEQLKITVVP VVAAAEDDDN EQHEEKAAEG EEKEEENGDE DEDEDEDEDD DDDDDEDEEE EEEVTDQLED LREHFKNTE EGKALVHHYE ECAERVKIQQ QQPGYADLEH KEDCVEEFFH LQHYLDTATA PRLFDKLK

UniProtKB: Cytochrome b-c1 complex subunit 6, mitochondrial

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Macromolecule #8: Cytochrome b-c1 complex subunit 8, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 8, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 10.987511 KDa
SequenceString:
MGPPSGKTYM GWWGHMGGPK QKGITSYAVS PYAQKPLQGI FHNAVFNSFR RFKSQFLYVL IPAGIYWYWW KNGNEYNEFL YSKAGREEL ERVNV

UniProtKB: Cytochrome b-c1 complex subunit 8, mitochondrial

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Macromolecule #9: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 43.68659 KDa
SequenceString: MAFRKSNVYL SLVNSYIIDS PQPSSINYWW NMGSLLGLCL VIQIVTGIFM AMHYSSNIEL AFSSVEHIMR DVHNGYILRY LHANGASFF FMVMFMHMAK GLYYGSYRSP RVTLWNVGVI IFILTIATAF LGYCCVYGQM SHWGATVITN LFSAIPFVGN D IVSWLWGG ...String:
MAFRKSNVYL SLVNSYIIDS PQPSSINYWW NMGSLLGLCL VIQIVTGIFM AMHYSSNIEL AFSSVEHIMR DVHNGYILRY LHANGASFF FMVMFMHMAK GLYYGSYRSP RVTLWNVGVI IFILTIATAF LGYCCVYGQM SHWGATVITN LFSAIPFVGN D IVSWLWGG FSVSNPTIQR FFALHYLVPF IIAAMVIMHL MALHIHGSSN PLGITGNLDR IPMHSYFIFK DLVTVFLFML IL ALFVFYS PNTLGHPDNY IPGNPLVTPA SIVPEWYLLP FYAILRSIPD KLLGVITMFA AILVLLVLPF TDRSVVRGNT FKV LSKFFF FIFVFNFVLL GQIGACHVEV PYVLMGQIAT FIYFAYFLII VPVISTIENV LFYIGRVNK

UniProtKB: Cytochrome b

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Macromolecule #10: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 58.832586 KDa
SequenceString: MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFFL VMPALIGGFG NYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV ESGAGTGWTV YPPLSSIQAH SGPSVDLAIF ALHLTSISSL L GAINFIVT ...String:
MVQRWLYSTN AKDIAVLYFM LAIFSGMAGT AMSLIIRLEL AAPGSQYLHG NSQLFNVLVV GHAVLMIFFL VMPALIGGFG NYLLPLMIG ATDTAFPRIN NIAFWVLPMG LVCLVTSTLV ESGAGTGWTV YPPLSSIQAH SGPSVDLAIF ALHLTSISSL L GAINFIVT TLNMRTNGMT MHKLPLFVWS IFITAFLLLL SLPVLSAGIT MLLLDRNFNT SFFEVSGGGD PILYEHLFWF FG HPEVYIL IIPGFGIISH VVSTYSKKPV FGEISMVYAM ASIGLLGFLV WSHHMYIVGL DADTRAYFTS ATMIIAIPTG IKI FSWLAT IHGGSIRLAT PMLYAIAFLF LFTMGGLTGV ALANASLDVA FHDTYYVVGH FHYVLSMGAI FSLFAGYYYW SPQI LGLNY NEKLAQIQFW LIFIGANVIF FPMHFLGING MPRRIPDYPD AFAGWNYVAS IGSFIATLSL FLFIYILYDQ LVNGL NNKV NNKSVIYNKA PDFVESNTIF NLNTVKSSSI EFLLTSPPAV HSFNTPAVQS

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #11: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.097523 KDa
SequenceString: MFSNLSKRWA QRTLSKSFYS TATGAASKSG KLTQKLVTAG VAAAGITAST LLYADSLTAE AMTAAEHGLH APAYAWSHNG PFETFDHAS IRRGYQVYRE VCAACHSLDR VAWRTLVGVS HTNEEVRNMA EEFEYDDEPD EQGNPKKRPG KLSDYIPGPY P NEQAARAA ...String:
MFSNLSKRWA QRTLSKSFYS TATGAASKSG KLTQKLVTAG VAAAGITAST LLYADSLTAE AMTAAEHGLH APAYAWSHNG PFETFDHAS IRRGYQVYRE VCAACHSLDR VAWRTLVGVS HTNEEVRNMA EEFEYDDEPD EQGNPKKRPG KLSDYIPGPY P NEQAARAA NQGALPPDLS LIVKARHGGC DYIFSLLTGY PDEPPAGVAL PPGSNYNPYF PGGSIAMARV LFDDMVEYED GT PATTSQM AKDVTTFLNW CAEPEHDERK RLGLKTVIIL SSLYLLSIWV KKFKWAGIKT RKFVFNPPKP RK

UniProtKB: Cytochrome c1, heme protein, mitochondrial

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Macromolecule #12: Cytochrome c oxidase subunit 8, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 8, mitochondrial / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 8.921686 KDa
SequenceString:
MLCQQMIRTT AKRSSNIMTR PIIMKRSVHF KDGVYENIPF KVKGRKTPYA LSHFGFFAIG FAVPFVACYV QLKKSGAF

UniProtKB: Cytochrome c oxidase subunit 8, mitochondrial

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Macromolecule #13: Cytochrome c oxidase subunit 7, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7, mitochondrial / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 6.942349 KDa
SequenceString:
MANKVIQLQK IFQSSTKPLW WRHPRSALYL YPFYAIFAVA VVTPLLYIPN AIRGIKAKKA

UniProtKB: Cytochrome c oxidase subunit 7, mitochondrial

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Macromolecule #14: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.383582 KDa
SequenceString: MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDIV AEATYLGDHT MAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT LGACWPPVGI EAVQPTELPL LNTIILLSSG ATVTYSHHAL I AGNRNKAL ...String:
MTHLERSRHQ QHPFHMVMPS PWPIVVSFAL LSLALSTALT MHGYIGNMNM VYLALFVLLT SSILWFRDIV AEATYLGDHT MAVRKGINL GFLMFVLSEV LIFAGLFWAY FHSAMSPDVT LGACWPPVGI EAVQPTELPL LNTIILLSSG ATVTYSHHAL I AGNRNKAL SGLLITFWLI VIFVTCQYIE YTNAAFTISD GVYGSVFYAG TGLHFLHMVM LAAMLGVNYW RMRNYHLTAG HH VGYETTI IYTHVLDVIW LFLYVVFYWW GV

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #15: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.585055 KDa
SequenceString: MLDLLRLQLT TFIMNDVPTP YACYFQDSAT PNQEGILELH DNIMFYLLVI LGLVSWMLYT IVMTYSKNPI AYKYIKHGQT IEVIWTIFP AVILLIIAFP SFILLYLCDE VISPAMTIKA IGYQWYWKYE YSDFINDSGE TVEFESYVIP DELLEEGQLR L LDTDTSMV ...String:
MLDLLRLQLT TFIMNDVPTP YACYFQDSAT PNQEGILELH DNIMFYLLVI LGLVSWMLYT IVMTYSKNPI AYKYIKHGQT IEVIWTIFP AVILLIIAFP SFILLYLCDE VISPAMTIKA IGYQWYWKYE YSDFINDSGE TVEFESYVIP DELLEEGQLR L LDTDTSMV VPVDTHIRFV VTAADVIHDF AIPSLGIKVD ATPGRLNQVS ALIQREGVFY GACSELCGTG HANMPIKIEA VS LPKFLEW LNEQ

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #16: Cytochrome c oxidase subunit 6, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.3666 KDa
SequenceString:
MLSRAIFRNP VINRTLLRAR PGAYHATRLT KNTFIQSRKY SDAHDEETFE EFTARYEKEF DEAYDLFEVQ RVLNNCFSYD LVPAPAVIE KALRAARRVN DLPTAIRVFE ALKYKVENED QYKAYLDELK DVRQELGVPL KEELFPSSS

UniProtKB: Cytochrome c oxidase subunit 6, mitochondrial

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Macromolecule #17: Cytochrome c oxidase subunit 9, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 9, mitochondrial / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.974226 KDa
SequenceString:
MTIAPITGTI KRRVIMDIVL GFSLGGVMAS YWWWGFHMDK INKREKFYAE LAERKKQEN

UniProtKB: Cytochrome c oxidase subunit 9, mitochondrial

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Macromolecule #18: Cytochrome c oxidase subunit 13, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 13, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 15.046146 KDa
SequenceString:
MFRQCAKRYA SSLPPNALKP AFGPPDKVAA QKFKESLMAT EKHAKDTSNM WVKISVWVAL PAIALTAVNT YFVEKEHAEH REHLKHVPD SEWPRDYEFM NIRSKPFFWG DGDKTLFWNP VVNRHIEHDD

UniProtKB: Cytochrome c oxidase subunit 13, mitochondrial

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Macromolecule #19: Cytochrome c oxidase subunit 4, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.164557 KDa
SequenceString:
MLSLRQSIRF FKPATRTLCS SRYLLQQKPV VKTAQNLAEV NGPETLIGPG AKEGTVPTDL DQETGLARLE LLGKLEGIDV FDTKPLDSS RKGTMKDPII IESYDDYRYV GCTGSPAGSH TIMWLKPTVN EVARCWECGS VYKLNPVGVP NDDHHH

UniProtKB: Cytochrome c oxidase subunit 4, mitochondrial

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Macromolecule #20: Cytochrome c oxidase subunit 12, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 12, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.799895 KDa
SequenceString:
MADQENSPLH TVGFDARFPQ QNQTKHCWQS YVDYHKCVNM KGEDFAPCKV FWKTYNALCP LDWIEKWDDQ REKGIFAGDI NSD

UniProtKB: Cytochrome c oxidase subunit 12, mitochondrial

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Macromolecule #21: Cytochrome c oxidase subunit 26, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 26, mitochondrial / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.461718 KDa
SequenceString:
MFFSQVLRSS ARAAPIKRYT GGRIGESWVI TEGRRLIPEI FQWSAVLSVC LGWPGAVYFF SKARKA

UniProtKB: Cytochrome c oxidase subunit 26, mitochondrial

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Macromolecule #22: Cytochrome c oxidase subunit 5A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.161465 KDa
SequenceString:
MLRNTFTRAG GLSRITSVRF AQTHALSNAA VMDLQSRWEN MPSTEQQDIV SKLSERQKLP WAQLTEPEKQ AVWYISYGEW GPRRPVLNK GDSSFIAKGV AAGLLFSVGL FAVVRMAGGQ DAKTMNKEWQ LKSDEYLKSK NANPWGGYSQ VQSK

UniProtKB: Cytochrome c oxidase subunit 5A, mitochondrial

+
Macromolecule #23: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 23 / Number of copies: 24 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-PEF:
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

+
Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 24 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #25: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 25 / Number of copies: 10 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #26: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 26 / Number of copies: 6 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PCF:
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

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Macromolecule #27: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-penta...

MacromoleculeName: (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
type: ligand / ID: 27 / Number of copies: 1 / Formula: CN5
Molecular weightTheoretical: 634.631 Da
Chemical component information

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

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Macromolecule #28: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 28 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #29: 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)...

MacromoleculeName: 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
type: ligand / ID: 29 / Number of copies: 4 / Formula: UQ6
Molecular weightTheoretical: 592.891 Da
Chemical component information

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

+
Macromolecule #30: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 30 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #31: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 31 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #32: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 32 / Number of copies: 4 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 360 pixel / Digitization - Dimensions - Height: 360 pixel / Digitization - Frames/image: 1-35 / Number real images: 20253 / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1510025
Startup modelType of model: OTHER
Details: The initial model is generated from a subset of particles.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 493055
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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