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- EMDB-44770: Tethered respiratory III2IV2 supercomplex from Saccharomyces cere... -

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Basic information

Entry
Database: EMDB / ID: EMD-44770
TitleTethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae
Map dataSaccharomyces cerevisiae tethered supercomplex
Sample
  • Complex: Tethered supercomplex
    • Complex: Ubiquinol-cytochrome c oxidoreductase
      • Protein or peptide: x 10 types
    • Complex: Cytochrome c oxidase
      • Protein or peptide: x 11 types
  • Ligand: x 19 types
KeywordsComplex / Oxidoreductase / Respiration / ELECTRON TRANSPORT
Function / homology
Function and homology information


: / Complex III assembly / matrix side of mitochondrial inner membrane / : / mitochondrial respiratory chain complex IV 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 / : / mitochondrial respiratory chain complex IV assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex III assembly / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / respiratory chain complex III / cellular respiration / 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 / nuclear periphery / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / metalloendopeptidase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / maintenance of translational fidelity / mitochondrial membrane / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / membrane / 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 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 Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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 / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Cytochrome c oxidase subunit III-like superfamily / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome c/quinol oxidase subunit II / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome C oxidase subunit II, transmembrane domain superfamily / : / Cytochrome c1 / Cytochrome C1 family / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / : / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome b/b6, C-terminal / Cytochrome c oxidase-like, subunit I domain / Cytochrome b(C-terminal)/b6/petD / Cytochrome oxidase subunit I profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome C oxidase subunit II, periplasmic domain / Rieske iron-sulphur protein, C-terminal / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / 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 / 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 W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsEldeeb MH / Carlstrom A / Berndtsson J / Ott M / Fontanesi F
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W911NF-21-1-0359 United States
CitationJournal: Nat Commun / Year: 2026
Title: Mitochondrial respirasome-like supercomplexes support metabolic flexibility in yeast.
Authors: Mazzen H Eldeeb / Zoe Cosner / Andreas Carlström / Jeffri-Noelle Mays / Gabriella F Rodriguez / Jens Berndtsson / Martin Ott / Flavia Fontanesi /
Abstract: The mitochondrial respiratory chain (MRC) complexes, crucial for aerobic energy transduction in eukaryotes, form conserved higher-order structures called supercomplexes (SCs). The elucidation of SC ...The mitochondrial respiratory chain (MRC) complexes, crucial for aerobic energy transduction in eukaryotes, form conserved higher-order structures called supercomplexes (SCs). The elucidation of SC physiological relevance is critical for our understanding of mitochondrial function and bioenergetics but has been hindered by the limited availability of experimental models isolating SC formation as the sole variable. In baker's yeast, SCs comprise IIIIV and IIIIV configurations, which enhance respiratory rates by facilitating cytochrome c diffusion along the SC surface. However, the roles of distinct SC conformations and MRC plasticity remain unclear. To address these questions, we engineered a yeast strain expressing a covalently-linked IIIIV SC, structurally like the wild-type. Expression of this tethered SC supports robust respiratory activity but selectively impacts cytosolic NADH-driven respiration, due to distinct interactions with the NADH dehydrogenase Nde1. We propose that in yeast mitochondria, substrate-specific respirasome-like SCs contribute to the optimization of electron fluxes and support metabolic flexibility.
History
DepositionMay 7, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44770.png

Downloads & links

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Map

FileDownload / File: emd_44770.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSaccharomyces cerevisiae tethered supercomplex
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 450 pix.
= 508.05 Å		1.13 Å/pix.
x 450 pix.
= 508.05 Å		1.13 Å/pix.
x 450 pix.
= 508.05 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.129 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.0693736 - 3.231026
Average (Standard dev.)0.00038229115 (±0.08181127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 508.05 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Saccharomyces cerevisiae tethered supercomplex half map A

Fileemd_44770_half_map_1.map
AnnotationSaccharomyces cerevisiae tethered supercomplex half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Saccharomyces cerevisiae tethered supercomplex half map B

Fileemd_44770_half_map_2.map
AnnotationSaccharomyces cerevisiae tethered supercomplex half map B
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Tethered supercomplex

EntireName: Tethered supercomplex
Components
  • Complex: Tethered supercomplex
    • Complex: Ubiquinol-cytochrome c oxidoreductase
      • 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, mitochondrial
      • Protein or peptide: Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial
      • Protein or peptide: Cytochrome b-c1 complex subunit 8, mitochondrial
      • Protein or peptide: Cytochrome b-c1 complex subunit 9, mitochondrial
      • Protein or peptide: Cytochrome b-c1 complex subunit 10, mitochondrial
    • Complex: Cytochrome c oxidase
      • 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 subunit 5A, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 6, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 7, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 9, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 12, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 13, mitochondrial
      • Protein or peptide: Cytochrome c oxidase subunit 26, mitochondrial
  • Ligand: CARDIOLIPIN
  • Ligand: (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
  • 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: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
  • Ligand: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: CALCIUM ION
  • 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: MAGNESIUM ION
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: ZINC ION

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Supramolecule #1: Tethered supercomplex

SupramoleculeName: Tethered supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: W303

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Supramolecule #2: Ubiquinol-cytochrome c oxidoreductase

SupramoleculeName: Ubiquinol-cytochrome c oxidoreductase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: W303

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Supramolecule #3: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11-#21
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: W303

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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 W303 (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: 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 W303 (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

MacromoleculeName: Cytochrome b / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae W303 (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: Cytochrome c1, heme protein, mitochondrial

MacromoleculeName: Cytochrome c1, heme protein, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #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 W303 (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 #6: Cytochrome b-c1 complex subunit 6, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 6, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #7: Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxi...

MacromoleculeName: Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrial
type: protein_or_peptide / ID: 7
Details: Fusion protein composed of ubiquinol-cytochrome c oxidoreductase subunit 7 (Qcr7) fused by a linker (GGGGS) to a copy of cytochrome c oxidase subunit 8 (Cox8) without its mitochondrial ...Details: Fusion protein composed of ubiquinol-cytochrome c oxidoreductase subunit 7 (Qcr7) fused by a linker (GGGGS) to a copy of cytochrome c oxidase subunit 8 (Cox8) without its mitochondrial targeting sequence.,Fusion protein composed of ubiquinol-cytochrome c oxidoreductase subunit 7 (Qcr7) fused by a linker (GGGGS) to a copy of cytochrome c oxidase subunit 8 (Cox8) without its mitochondrial targeting sequence.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 20.618779 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae W303 (yeast)
SequenceString:
MPQSFTSIAR IGDYILKSPV LSKLCVPVAN QFINLAGYKK LGLKFDDLIA EENPIMQTAL RRLPEDESYA RAYRIIRAHQ TELTHHLLP RNEWIKAQED VPYLLPYILE AEAAAKEKDE LDNIEVSKGG GGSVHFKDGV YENIPFKVKG RKTPYALSHF G FFAIGFAV PFVACYVQLK KSGAF

UniProtKB: Cytochrome b-c1 complex subunit 7, mitochondrial, Cytochrome c oxidase subunit 8, 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 W303 (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-c1 complex subunit 9, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 9, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #10: Cytochrome b-c1 complex subunit 10, mitochondrial

MacromoleculeName: Cytochrome b-c1 complex subunit 10, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #11: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #12: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #13: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Saccharomyces cerevisiae W303 (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: Cytochrome c oxidase subunit 4, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 4, mitochondrial / type: protein_or_peptide / ID: 14 / Details: Subunit contains a FLAG tag. / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #15: Cytochrome c oxidase subunit 5A, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 5A, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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

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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 W303 (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 7, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 7, mitochondrial / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast)
Molecular weightTheoretical: 6.942349 KDa
SequenceString:
MANKVIQLQK IFQSSTKPLW WRHPRSALYL YPFYAIFAVA VVTPLLYIPN AIRGIKAKKA

UniProtKB: Cytochrome c oxidase subunit 7, mitochondrial

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Macromolecule #18: Cytochrome c oxidase subunit 9, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 9, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #19: Cytochrome c oxidase subunit 12, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 12, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #20: Cytochrome c oxidase subunit 13, mitochondrial

MacromoleculeName: Cytochrome c oxidase subunit 13, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae W303 (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 #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 W303 (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: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 22 / Number of copies: 8 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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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: (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: 24 / 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 #25: (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: 25 / 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 #26: 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: 26 / 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 #27: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 27 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #28: (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: 28 / 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

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Macromolecule #29: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 29 / Number of copies: 6 / Formula: PEF
Molecular weightTheoretical: 691.959 Da
Chemical component information

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

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Macromolecule #30: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 30 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #31: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 31 / 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 #32: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / type: ligand / ID: 32 / Number of copies: 8 / Formula: PCF
Molecular weightTheoretical: 734.039 Da
Chemical component information

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

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Macromolecule #33: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 33 / Number of copies: 10 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #34: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 34 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #35: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 35 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #36: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 36 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #37: (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: 37 / Number of copies: 2 / 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 #38: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 38 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #39: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 39 / Number of copies: 2 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #40: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 40 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris-HCl pH 7.5
150.0 mMNaClSodium chloride
1.0 mMC7H7FO2SPhenylmethylsulfonyl fluoride (PMSF)
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid (EDTA)
0.1 %C56H92O29Digitonin
150.0 ng/uLC120H169N31O49S3X FLAG peptide
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: The grid is covered with a 3 nm ultrathin carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details: 3 uL of sample, 5 s blot time, 30 s hold time, 0 blot force..

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12211 / Average exposure time: 2.6 sec. / Average electron dose: 55.452 e/Å2
Details: Images were collected as movies composed of 40 frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1646359
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial model for refinement was generated ab-initio in cryoSPARC.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 47746
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2) / Details: Non-uniform refinement
Final 3D classificationNumber classes: 5 / Avg.num./class: 9785 / Software - Name: cryoSPARC (ver. 4.2)
Details: Classification was performed in 3D to remove junk particles from the dataset. The final round of classification used 48,925 particles, with 48,218 ultimately being used for refinement of the predominant class.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6ymx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-9bpb:
Tethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae

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