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- EMDB-0004: Saccharomyces cerevisiae respiratory supercomplex III2IV -

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Basic information

Entry
Database: EMDB / ID: EMD-0004
TitleSaccharomyces cerevisiae respiratory supercomplex III2IV
Map dataModelling map
Sample
  • Complex: Saccharomyces cerevisiae Supercomplex (III2IV)
    • Complex: Saccharomyces cerevisiae complex III
      • Protein or peptide: x 10 types
    • Complex: Saccharomyces cerevisiae complex IV
      • Protein or peptide: x 12 types
  • Ligand: x 13 types
KeywordsRespiratory chain / supercomplex / bc1 complex / cytochrome c oxidase / ELECTRON TRANSPORT
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 / 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 / electron transfer activity / 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 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
Similarity search - Domain/homology
Cytochrome c oxidase subunit 3 / Cytochrome b / Cytochrome c oxidase subunit 2 / quinol--cytochrome-c reductase / : / : / : / : / : / BJ4_G0018620.mRNA.1.CDS.1 ...Cytochrome c oxidase subunit 3 / Cytochrome b / Cytochrome c oxidase subunit 2 / quinol--cytochrome-c reductase / : / : / : / : / : / BJ4_G0018620.mRNA.1.CDS.1 / : / : / : / : / : / : / : / : / : / : / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast) / Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsRathore S / Berndtsson J
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM structure of the yeast respiratory supercomplex.
Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott /
Abstract: Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes ...Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes IIIIV and IIIIV, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.
History
DepositionMay 15, 2018-
Header (metadata) releaseJul 18, 2018-
Map releaseJan 2, 2019-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0004.png

Downloads & links

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Map

FileDownload / File: emd_0004.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationModelling map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 370 pix.
= 392.2 Å		1.06 Å/pix.
x 370 pix.
= 392.2 Å		1.06 Å/pix.
x 370 pix.
= 392.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-1.2225217 - 2.422639
Average (Standard dev.)0.008202017 (±0.08052676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 392.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Halfmap1

Fileemd_0004_half_map_1.map
AnnotationHalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap2

Fileemd_0004_half_map_2.map
AnnotationHalfmap2
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae Supercomplex (III2IV)

EntireName: Saccharomyces cerevisiae Supercomplex (III2IV)
Components
  • Complex: Saccharomyces cerevisiae Supercomplex (III2IV)
    • Complex: Saccharomyces cerevisiae complex III
      • Protein or peptide: BJ4_G0001550.mRNA.1.CDS.1
      • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
      • Protein or peptide: Cytochrome b
      • Protein or peptide: BJ4_G0049990.mRNA.1.CDS.1
      • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
      • Protein or peptide: QCR6 isoform 1
      • Protein or peptide: Complex III subunit 7
      • Protein or peptide: BJ4_G0028260.mRNA.1.CDS.1
      • Protein or peptide: HLJ1_G0021680.mRNA.1.CDS.1
      • Protein or peptide: BJ4_G0023510.mRNA.1.CDS.1
    • Complex: Saccharomyces cerevisiae complex IV
      • Protein or peptide: Cytochrome c oxidase subunit 1
      • Protein or peptide: Cytochrome c oxidase subunit 2
      • Protein or peptide: Cytochrome c oxidase subunit 3
      • Protein or peptide: BJ4_G0018620.mRNA.1.CDS.1
      • Protein or peptide: BJ4_G0046460.mRNA.1.CDS.1
      • Protein or peptide: BJ4_G0024040.mRNA.1.CDS.1
      • Protein or peptide: BJ4_G0043230.mRNA.1.CDS.1
      • Protein or peptide: BJ4_G0038800.mRNA.1.CDS.1
      • Protein or peptide: Cytochrome c oxidase polypeptide VIIA
      • Protein or peptide: BJ4_G0035470.mRNA.1.CDS.1
      • Protein or peptide: Cytochrome c oxidase subunit
      • Protein or peptide: Unknown Cox subunit
  • Ligand: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
  • Ligand: HEME C
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
  • 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: 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: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
  • Ligand: (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
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: DINUCLEAR COPPER ION

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Supramolecule #1: Saccharomyces cerevisiae Supercomplex (III2IV)

SupramoleculeName: Saccharomyces cerevisiae Supercomplex (III2IV) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria

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Supramolecule #2: Saccharomyces cerevisiae complex III

SupramoleculeName: Saccharomyces cerevisiae complex III / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria

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Supramolecule #3: Saccharomyces cerevisiae complex IV

SupramoleculeName: Saccharomyces cerevisiae complex IV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11-#22
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria

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Macromolecule #1: BJ4_G0001550.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0001550.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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: UNIPROTKB: A0A6A5Q3X1

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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: UNIPROTKB: A0A6A5Q625

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Macromolecule #3: Cytochrome b

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
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 #4: BJ4_G0049990.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0049990.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
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: quinol--cytochrome-c reductase

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

MacromoleculeName: Cytochrome b-c1 complex subunit Rieske, mitochondrial / type: protein_or_peptide / ID: 5 / 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: UNIPROTKB: A0A6A5PX11

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Macromolecule #6: QCR6 isoform 1

MacromoleculeName: QCR6 isoform 1 / type: protein_or_peptide / ID: 6 / 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: UNIPROTKB: A0A6A5Q022

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Macromolecule #7: Complex III subunit 7

MacromoleculeName: Complex III subunit 7 / type: protein_or_peptide / ID: 7 / 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: UNIPROTKB: A0A6A5Q2H4

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Macromolecule #8: BJ4_G0028260.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0028260.mRNA.1.CDS.1 / 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: UNIPROTKB: A0A6A5PU80

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Macromolecule #9: HLJ1_G0021680.mRNA.1.CDS.1

MacromoleculeName: HLJ1_G0021680.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 9 / 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: UNIPROTKB: A0A6L0Z0I8

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Macromolecule #10: BJ4_G0023510.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0023510.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 10 / 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: UNIPROTKB: A0A6L0ZE60

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Macromolecule #11: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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 #12: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
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

+
Macromolecule #13: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
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 #14: BJ4_G0018620.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0018620.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / 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: BJ4_G0018620.mRNA.1.CDS.1

+
Macromolecule #15: BJ4_G0046460.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0046460.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / 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: UNIPROTKB: A0A6A5Q8F6

+
Macromolecule #16: BJ4_G0024040.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0024040.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / 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: UNIPROTKB: A0A6A5PUE0

+
Macromolecule #17: BJ4_G0043230.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0043230.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.942349 KDa
SequenceString:
MANKVIQLQK IFQSSTKPLW WRHPRSALYL YPFYAIFAVA VVTPLLYIPN AIRGIKAKKA

UniProtKB: UNIPROTKB: A0A6A5PQU1

+
Macromolecule #18: BJ4_G0038800.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0038800.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / 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: UNIPROTKB: A0A6A5PRD8

+
Macromolecule #19: Cytochrome c oxidase polypeptide VIIA

MacromoleculeName: Cytochrome c oxidase polypeptide VIIA / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 6.974226 KDa
SequenceString:
MTIAPITGTI KRRVIMDIVL GFSLGGVMAS YWWWGFHMDK INKREKFYAE LAERKKQEN

UniProtKB: UNIPROTKB: A0A6A5Q104

+
Macromolecule #20: BJ4_G0035470.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0035470.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / 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: UNIPROTKB: A0A6A5PU81

+
Macromolecule #21: Cytochrome c oxidase subunit

MacromoleculeName: Cytochrome c oxidase subunit / type: protein_or_peptide / ID: 21 / Number of copies: 1 / 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: UNIPROTKB: A0A6A5PWA0

+
Macromolecule #22: Unknown Cox subunit

MacromoleculeName: Unknown Cox subunit / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.656265 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #23: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate

MacromoleculeName: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
type: ligand / ID: 23 / Number of copies: 2 / Formula: 6PH
Molecular weightTheoretical: 592.785 Da
Chemical component information

ChemComp-6PH:
(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate

+
Macromolecule #24: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 24 / Number of copies: 6 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #25: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...

MacromoleculeName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
type: ligand / ID: 25 / Number of copies: 2 / Formula: 8PE
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-8PE:
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / phospholipid*YM

+
Macromolecule #26: (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: 26 / 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

+
Macromolecule #27: 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: 27 / Number of copies: 2 / 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 #28: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate

MacromoleculeName: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
type: ligand / ID: 28 / Number of copies: 2 / Formula: 7PH
Molecular weightTheoretical: 564.732 Da
Chemical component information

ChemComp-7PH:
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate

+
Macromolecule #29: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 29 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

+
Macromolecule #30: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 30 / Number of copies: 2 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

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

+
Macromolecule #31: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoy...

MacromoleculeName: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
type: ligand / ID: 31 / Number of copies: 2 / Formula: 9PE
Molecular weightTheoretical: 593.773 Da
Chemical component information

ChemComp-9PE:
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / phospholipid*YM

+
Macromolecule #32: (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16...

MacromoleculeName: (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
type: ligand / ID: 32 / Number of copies: 1 / Formula: CN3
Molecular weightTheoretical: 834.862 Da
Chemical component information

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

+
Macromolecule #33: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 33 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

+
Macromolecule #34: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 34 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

+
Macromolecule #35: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 35 / Number of copies: 1 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: ABINITIO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 203271
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Target criteria: Cross-Correlation coefficient
Output model

PDB-6giq:
Saccharomyces cerevisiae respiratory supercomplex III2IV

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