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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
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 / mitochondrial respirasome assembly / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / cellular respiration / cytochrome-c oxidase ...mitochondrial cytochrome c oxidase assembly / matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / mitochondrial respirasome assembly / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / cellular respiration / cytochrome-c oxidase / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / proton transmembrane transport / nuclear periphery / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily ...Cytochrome c oxidase subunit VII, budding yeast / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome b-c1 complex subunit 10, fungi / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / : / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Va / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome c oxidase subunit III / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Heme-copper oxidase subunit III family profile. / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome c oxidase subunit III-like superfamily / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b / : / : / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Copper centre Cu(A) / Cytochrome C oxidase subunit II, transmembrane domain superfamily / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Rieske iron-sulphur protein, C-terminal / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / 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
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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast) / Baker's yeast (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsRathore S / Berndtsson J / Conrad J / Ott M
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-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6giq
  • Surface level: 0.33
  • Imaged by UCSF Chimera
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Movie viewer
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
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.33 / Movie #1: 0.4
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 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z392.200392.200392.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-1.2232.4230.008

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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
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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: Cytochrome b-c1 complex subunit 1, mitochondrial
      • Protein or peptide: Cytochrome b-c1 complex subunit 2, mitochondrial
      • Protein or peptide: Cytochrome b
      • Protein or peptide: Cytochrome c1, heme protein, mitochondrial
      • Protein or peptide: Cytochrome b-c1 complex subunit Rieske, mitochondrial
      • Protein or peptide: Cytochrome b-c1 complex subunit 6
      • Protein or peptide: Cytochrome b-c1 complex subunit 7
      • Protein or peptide: Cytochrome b-c1 complex subunit 8
      • Protein or peptide: Cytochrome b-c1 complex subunit 9
      • Protein or peptide: Cytochrome b-c1 complex subunit 10
    • 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: Cytochrome c oxidase subunit 4, mitochondrial
      • Protein or peptide: Cytochrome c oxidase polypeptide 5A, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 6, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 7
      • Protein or peptide: Cytochrome c oxidase polypeptide VIII, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 7A
      • Protein or peptide: Cytochrome c oxidase subunit 6B
      • Protein or peptide: Cytochrome c oxidase subunit 6A, mitochondrial
      • Protein or peptide: Unknown Cox subunit
  • Ligand: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • 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: 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: Baker's yeast (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

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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: Baker's yeast (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

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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: Baker's yeast (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

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Macromolecule #4: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (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

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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: Baker's yeast (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

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Macromolecule #6: Cytochrome b-c1 complex subunit 6

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

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Macromolecule #7: Cytochrome b-c1 complex subunit 7

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

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Macromolecule #8: Cytochrome b-c1 complex subunit 8

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

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Macromolecule #9: Cytochrome b-c1 complex subunit 9

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

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Macromolecule #10: Cytochrome b-c1 complex subunit 10

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

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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: Baker's yeast (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

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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 / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (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

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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 / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (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

+
Macromolecule #14: Cytochrome c oxidase subunit 4, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (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

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Macromolecule #15: Cytochrome c oxidase polypeptide 5A, mitochondrial

MacromoleculeName: Cytochrome c oxidase polypeptide 5A, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (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

+
Macromolecule #16: Cytochrome c oxidase subunit 6, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 17.3666 KDa
SequenceString:
MLSRAIFRNP VINRTLLRAR PGAYHATRLT KNTFIQSRKY SDAHDEETFE EFTARYEKEF DEAYDLFEVQ RVLNNCFSYD LVPAPAVIE KALRAARRVN DLPTAIRVFE ALKYKVENED QYKAYLDELK DVRQELGVPL KEELFPSSS

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Macromolecule #17: Cytochrome c oxidase subunit 7

MacromoleculeName: Cytochrome c oxidase subunit 7 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 6.942349 KDa
SequenceString:
MANKVIQLQK IFQSSTKPLW WRHPRSALYL YPFYAIFAVA VVTPLLYIPN AIRGIKAKKA

+
Macromolecule #18: Cytochrome c oxidase polypeptide VIII, mitochondrial

MacromoleculeName: Cytochrome c oxidase polypeptide VIII, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 8.921686 KDa
SequenceString:
MLCQQMIRTT AKRSSNIMTR PIIMKRSVHF KDGVYENIPF KVKGRKTPYA LSHFGFFAIG FAVPFVACYV QLKKSGAF

+
Macromolecule #19: Cytochrome c oxidase subunit 7A

MacromoleculeName: Cytochrome c oxidase subunit 7A / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 6.974226 KDa
SequenceString:
MTIAPITGTI KRRVIMDIVL GFSLGGVMAS YWWWGFHMDK INKREKFYAE LAERKKQEN

+
Macromolecule #20: Cytochrome c oxidase subunit 6B

MacromoleculeName: Cytochrome c oxidase subunit 6B / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 9.799895 KDa
SequenceString:
MADQENSPLH TVGFDARFPQ QNQTKHCWQS YVDYHKCVNM KGEDFAPCKV FWKTYNALCP LDWIEKWDDQ REKGIFAGDI NSD

+
Macromolecule #21: Cytochrome c oxidase subunit 6A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 6A, mitochondrial / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Baker's yeast (brewer's yeast)
Molecular weightTheoretical: 15.046146 KDa
SequenceString:
MFRQCAKRYA SSLPPNALKP AFGPPDKVAA QKFKESLMAT EKHAKDTSNM WVKISVWVAL PAIALTAVNT YFVEKEHAEH REHLKHVPD SEWPRDYEFM NIRSKPFFWG DGDKTLFWNP VVNRHIEHDD

+
Macromolecule #22: Unknown Cox subunit

MacromoleculeName: Unknown Cox subunit / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Baker's yeast (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 / Phosphatidic acid

+
Macromolecule #24: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 24 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
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 / Cardiolipin

+
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 / Phosphatidic acid

+
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 / Iron–sulfur 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 / Dipalmitoylphosphatidylcholine

+
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 / Cardiolipin

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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 / Copper

+
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 / 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

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

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

-
Image processing

Startup modelType of model: OTHER / Details: ABINITIO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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
FSC plot (resolution estimation)

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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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