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- EMDB-13977: Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV... -

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Basic information

Entry
Database: EMDB / ID: EMD-13977
TitleCytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (as isolated)
Map dataphenix density modified map
Sample
  • Complex: cytochrome bcc-aa3 supercomplex
    • Protein or peptide: x 13 types
  • Ligand: x 20 types
Keywordssupercomplex / respiratory chain / cytochrome bcc-aa3 supercomplex / proton translocation / bioenergetics / membrane protein / electron transport / OXIDOREDUCTASE
Function / homology
Function and homology information


thiamine biosynthetic process / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ATP synthesis coupled electron transport ...thiamine biosynthetic process / aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / electron transport coupled proton transport / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ATP synthesis coupled electron transport / respiratory electron transport chain / monooxygenase activity / electron transport chain / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / Neocarzinostatin-like / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB / Cytochrome c oxidase, subunit I bacterial type ...Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / Neocarzinostatin-like / Cytochrome bc1 complex, cytochrome c subunit / Cytochrome c oxidase subunit IV, actinobacteria / QcrA subunit, N-terminal / Cytochrome c oxidase subunit IV / QcrA subunit N-terminal region / Cytochrome b(N-terminal)/b6/petB / Cytochrome c oxidase, subunit I bacterial type / : / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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 c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / 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. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Cytochrome c / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Thiamine biosynthesis protein X / Cytochrome c oxidase subunit 1 / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Uncharacterized protein Cgl2664/cg2949 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide 4 / Cytochrome bc1 complex cytochrome c subunit / Uncharacterized membrane protein Cgl2017/cg2211 / Uncharacterized protein ...Thiamine biosynthesis protein X / Cytochrome c oxidase subunit 1 / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Uncharacterized protein Cgl2664/cg2949 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide 4 / Cytochrome bc1 complex cytochrome c subunit / Uncharacterized membrane protein Cgl2017/cg2211 / Uncharacterized protein / Hypothetical membrane protein / Hypothetical membrane protein / Cytochrome c oxidase subunit 3
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKao W-C / Hunte C
Funding support Germany, France, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)BIOSS EXC-294 Germany
German Research Foundation (DFG)CIBSS EXC-2189 Project ID 390939984 Germany
German Research Foundation (DFG)Project-ID 403222702 / SFB 1381 Germany
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-01 France
German Research Foundation (DFG)SCHI 871/11-1 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for safe and efficient energy conversion in a respiratory supercomplex.
Authors: Wei-Chun Kao / Claire Ortmann de Percin Northumberland / Tat Cheung Cheng / Julio Ortiz / Alexandre Durand / Ottilie von Loeffelholz / Oliver Schilling / Martin L Biniossek / Bruno P Klaholz / Carola Hunte /
Abstract: Proton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species ...Proton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species during aerobic cellular respiration. Cytochrome bc complexes and cytochrome aa oxidases are major drivers of the proton motive force that fuels ATP generation via respiration, but how wasteful electron- and proton transfer is controlled to enhance safety and efficiency in the context of supercomplexes is not known. Here, we address this question with the 2.8 Å resolution cryo-EM structure of the cytochrome bcc-aa (III-IV) supercomplex from the actinobacterium Corynebacterium glutamicum. Menaquinone, substrate mimics, lycopene, an unexpected Q site, dioxygen, proton transfer routes, and conformational states of key protonable residues are resolved. Our results show how safe and efficient energy conversion is achieved in a respiratory supercomplex through controlled electron and proton transfer. The structure may guide the rational design of drugs against actinobacteria that cause diphtheria and tuberculosis.
History
DepositionDec 13, 2021-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13977.png

Downloads & links

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Map

FileDownload / File: emd_13977.map.gz / Format: CCP4 / Size: 28.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphenix density modified map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 215 pix.
= 232.2 Å		1.08 Å/pix.
x 231 pix.
= 249.48 Å		1.08 Å/pix.
x 150 pix.
= 162. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.79843307 - 2.0563803
Average (Standard dev.)0.000000000000323 (±0.09285805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin141182149
Dimensions231150215
Spacing215231150
CellA: 232.20001 Å / B: 249.48001 Å / C: 162.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : cytochrome bcc-aa3 supercomplex

EntireName: cytochrome bcc-aa3 supercomplex
Components
  • Complex: cytochrome bcc-aa3 supercomplex
    • Protein or peptide: Cytochrome bc1 complex Rieske iron-sulfur subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome b subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • 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 polypeptide 4
    • Protein or peptide: Uncharacterized protein Cgl2664/cg2949
    • Protein or peptide: Uncharacterized membrane protein Cgl2017/cg2211
    • Protein or peptide: Hypothetical membrane protein
    • Protein or peptide: Actinobacterial supercomplex, subunit C (AscC)
    • Protein or peptide: Hypothetical membrane protein
    • Protein or peptide: Thiamine biosynthesis protein X
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: [(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate
  • Ligand: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
  • Ligand: MENAQUINONE-9
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARDIOLIPIN
  • Ligand: LYCOPENE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: HEME C
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: HEME-AS
  • Ligand: COPPER (II) ION
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
  • Ligand: DINUCLEAR COPPER ION
  • Ligand: DIACYL GLYCEROL
  • Ligand: PALMITIC ACID
  • Ligand: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{S})-10-methylhenicosanoate
  • Ligand: water

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Supramolecule #1: cytochrome bcc-aa3 supercomplex

SupramoleculeName: cytochrome bcc-aa3 supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 / Details: Cofactor-containing respiratory supercomplex
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)

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Macromolecule #1: Cytochrome bc1 complex Rieske iron-sulfur subunit

MacromoleculeName: Cytochrome bc1 complex Rieske iron-sulfur subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 45.232207 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: MSNNNDKQYT TQELNAMSNE DLARLGTELD DVTIAYRKER FPIANDPAEK RAARAVTFWL VLGIIGGLGF LATYIFWPWE YKAHGDEGL LAYTLYTPML GITSGLCILS LGFAVVLYVK KFIPEEIAVQ RRHDGPSEEV DRRTIVALLN DSWQTSTLGR R KLIMGLAG ...String:
MSNNNDKQYT TQELNAMSNE DLARLGTELD DVTIAYRKER FPIANDPAEK RAARAVTFWL VLGIIGGLGF LATYIFWPWE YKAHGDEGL LAYTLYTPML GITSGLCILS LGFAVVLYVK KFIPEEIAVQ RRHDGPSEEV DRRTIVALLN DSWQTSTLGR R KLIMGLAG GGAVLAGLTI IAPMGGMIKN PWNPKEGPMD VQGDGTLWTS GWTLVENDVK VYLGRDTAAI AESHTDATGE HW STTGVSR LVRMRPEDLA AASMETVFPL PAEMVNDGAE YDPAKDVYEH QMHSVHGPRN AVMLIRLRTA DAEKVIEREG QES FHYGDY YAYSKICTHI GCPTSLYEAQ TNRILCPCHQ SQFDALHYGK PVFGPAARAL PQLPITVDEE GYLIAAGNFI EPLG PAFWE RKS

UniProtKB: Cytochrome bc1 complex Rieske iron-sulfur subunit

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Macromolecule #2: Cytochrome bc1 complex cytochrome b subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome b subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 59.863699 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: MSLATVGNNL DSRYTMASGI RRQINKVFPT HWSFMLGEIA LYSFIVLLLT GVYLTLFFDP SITKVIYDGG YLPLNGVEMS RAYATALDI SFEVRGGLFI RQMHHWAALL FVVSMLVHML RIFFTGAFRR PREANWIIGV VLIILGMAEG FMGYSLPDDL L SGVGLRIM ...String:
MSLATVGNNL DSRYTMASGI RRQINKVFPT HWSFMLGEIA LYSFIVLLLT GVYLTLFFDP SITKVIYDGG YLPLNGVEMS RAYATALDI SFEVRGGLFI RQMHHWAALL FVVSMLVHML RIFFTGAFRR PREANWIIGV VLIILGMAEG FMGYSLPDDL L SGVGLRIM SAIIVGLPII GTWMHWLIFG GDFPSDLMLD RFYIAHVLII PAILLGLIAA HLALVWYQKH TQFPGAGRTE NN VIGIRIM PLFAVKAVAF GLIVFGFLAL LAGVTTINAI WNLGPYNPSQ VSAGSQPDVY MLWTDGAARV MPAWELYLGN YTI PAVFWV AVMLGILVVL LVTYPFIERK FTGDDAHHNL LQRPRDVPVR TSLGVMALVF YILLTVSGGN DVYAMQFHVS LNAM TWIGR IGLIVGPAIA YFITYRLCIG LQRSDREVLE HGIETGIIKQ MPNGAFIEVH QPLGPVDDHG HPIPLPYAGA AVPKQ MNQL GYAEVETRGG FFGPDPEDIR AKAKEIEHAN HIEEANTLRA LNEANIERDK NEGKN

UniProtKB: Cytochrome bc1 complex cytochrome b subunit

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Macromolecule #3: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 29.89885 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: MAKPSAKKVK NRRKVRRTVA GALALTIGLS GAGILATAIT PDAQVATAQR DDQALISEGK DLYDVACITC HGVNLQGVED RGPSLVGVG EGAVYFQVHS GRMPILRNEA QAERKAPRYT EAQTLAIAAY VAANGGGPGL VYNEDGTLAM EELRGENYDG Q ITSADVAR ...String:
MAKPSAKKVK NRRKVRRTVA GALALTIGLS GAGILATAIT PDAQVATAQR DDQALISEGK DLYDVACITC HGVNLQGVED RGPSLVGVG EGAVYFQVHS GRMPILRNEA QAERKAPRYT EAQTLAIAAY VAANGGGPGL VYNEDGTLAM EELRGENYDG Q ITSADVAR GGDLFRLNCA SCHNFTGRGG ALSSGKYAPN LDAANEQEIY QAMLTGPQNM PKFSDRQLSA DEKKDIIAFI KS TKETPSP GGYSLGSLGP VAEGLFMWVF GILVLVAAAM WIGSRS

UniProtKB: Cytochrome bc1 complex cytochrome c subunit

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Macromolecule #4: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 66.340164 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: MTAVAPRVDG HVAPQRPEPT GHARKGSKAW LMMTTTDHKQ LGIMYIIMSF SFFFLGGLMA LLIRAELFTP GLQFLSNEQF NQLFTMHGT VMLLLYGTPI VWGFANYVLP LQIGAPDVAF PRLNAFGFWI TTVGGVAMLT GFLTPGGAAD FGWTMYSPLS D AIHSPGLG ...String:
MTAVAPRVDG HVAPQRPEPT GHARKGSKAW LMMTTTDHKQ LGIMYIIMSF SFFFLGGLMA LLIRAELFTP GLQFLSNEQF NQLFTMHGT VMLLLYGTPI VWGFANYVLP LQIGAPDVAF PRLNAFGFWI TTVGGVAMLT GFLTPGGAAD FGWTMYSPLS D AIHSPGLG SDMWIVGVGA TGIGSVASAI NMLTTILCLR APGMTMFRMP IFTWNIFVVS VLALLIFPLL LAAALGVLYD RK LGGHLYD PANGGSLLWQ HLFWFFGHPE VYVLALPFFG IVSEIIPVFS RKPMFGYVGL IFATLSIGAL SMAVWAHHMF VTG AVLLPF FSFMTFLISV PTGVKFFNWV GTMWKGHITW ETPMIWSVGF MATFLFGGLT GIMLASPPLD FHLADSYFLI AHFH YTLFG TVVFASCAGV YFWFPKMTGR MMDERLGKIH FWLTFVGFHG TFLIQHWVGN MGMPRRYADY LDSDGFTIYN QISTV FSFL LGLSVIPFIW NVFKSWRYGE LVTVDDPWGY GNSLEWATSC PPPRHNFASL PRIRSERPAF ELHYPHMIER MRAEAH TGH HDDINAPELG TAPALASDSS RAAWSHPQFE K

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #5: Cytochrome c oxidase subunit 2

MacromoleculeName: Cytochrome c oxidase subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 36.811105 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: CEVAPPGGVL GDFLRMGWPD GITPEAVAMG NFWSWVWVAA WIIGIIMWGL FLTAIFAWGA KRAEKRGEGE FPKQLQYNVP LELVLTIVP IIIVMVLFFF TVQTQDKVTA LDKNPEVTVD VTAYQWNWKF GYSEIDGSLA PGGQDYQGSD PERQAAAEAS K KDPSGDNP ...String:
CEVAPPGGVL GDFLRMGWPD GITPEAVAMG NFWSWVWVAA WIIGIIMWGL FLTAIFAWGA KRAEKRGEGE FPKQLQYNVP LELVLTIVP IIIVMVLFFF TVQTQDKVTA LDKNPEVTVD VTAYQWNWKF GYSEIDGSLA PGGQDYQGSD PERQAAAEAS K KDPSGDNP IHGNSKSDVS YLEFNRIETL GTTDEIPVMV LPVNTPIEFN LASADVAHSF WVPEFLFKRD AYAHPEANKS QR VFQIEEI TEEGAFVGRC AEMCGTYHAM MNFELRVVDR DSFAEYISFR DSNPDATNAQ ALEHIGQAPY ATSTSPFVSD RTA TRDGEN TQSNA

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #6: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 22.457217 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: MTSAVGNTGM AAPQRVAALN RPNMVSVGTI VFLSQELMFF AGLFAMYFVS RANGLANGSW GEQTDHLNVP YALLITVILV SSSVTCQFG VFAAERGDVY GLRKWFLVTI ILGSIFVIGQ GYEYITLVGH GLTIQSSVYG SAFFITTGFH ALHVIAGVMA F VVVLMRIH ...String:
MTSAVGNTGM AAPQRVAALN RPNMVSVGTI VFLSQELMFF AGLFAMYFVS RANGLANGSW GEQTDHLNVP YALLITVILV SSSVTCQFG VFAAERGDVY GLRKWFLVTI ILGSIFVIGQ GYEYITLVGH GLTIQSSVYG SAFFITTGFH ALHVIAGVMA F VVVLMRIH KSKFTPAQAT AAMVVSYYWH FVDVVWIGLF ITIYFIQ

UniProtKB: Cytochrome c oxidase subunit 3

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Macromolecule #7: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 15.557285 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
MKSSAKLMYG PTVFMAAMAV IYIFATMHVS DGGSVKGVEW VGSVALVLSA GLTLMLGVYL HFTEVRVDVL PEDWEEAEVA DKAGTLGFF SPSSIWPAAM SGAVGFLAFG VVYFHYWMIA VGLMLLIFTI TKLNLQYGVP KEKH

UniProtKB: Cytochrome c oxidase polypeptide 4

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Macromolecule #8: Uncharacterized protein Cgl2664/cg2949

MacromoleculeName: Uncharacterized protein Cgl2664/cg2949 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 16.954213 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
CSAGQITQTS SQVAAVDGNQ AGSANDPVLV RDVTVHLTTD GEAGVKFTAI NQDTSHTSHT LESVTVDGEE VELDDAEPIE RNCSLVADI QSELDLIEEP EVGCIQHVAT SLENPGFAYG GVVPVEFVFD TGAITIDATV SAPVLESGVE NREVGGDTAE A SHH

UniProtKB: Uncharacterized protein Cgl2664/cg2949

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Macromolecule #9: Uncharacterized membrane protein Cgl2017/cg2211

MacromoleculeName: Uncharacterized membrane protein Cgl2017/cg2211 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 16.385588 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
MAGSSHTIEP EIYRGVSTLD EPSAAWGWHG LKRNTIQLAG WISVLFMLGY NFGNHKGHVE TIWLLVITAL LVIGLLIHLF EPKLSQVRT ITSRNKPVGH VEPDWTYDQA TLTGTWGNLT DSQLRSVNIE PSRVAHLRAA DSAKELDN

UniProtKB: Uncharacterized membrane protein Cgl2017/cg2211

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Macromolecule #10: Hypothetical membrane protein

MacromoleculeName: Hypothetical membrane protein / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 12.14416 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
MNTMSSAKKK PAPERMHYIK GYVPVAYSSP HSSLERSATW LGMGFLLTAL AGVGAVLFAV GANSVGQQQE HWVLYSIIGV VFAVVCTVL GTVLIIKGRA PYNRYVKETG RTQ

UniProtKB: Hypothetical membrane protein

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Macromolecule #11: Actinobacterial supercomplex, subunit C (AscC)

MacromoleculeName: Actinobacterial supercomplex, subunit C (AscC) / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 8.373271 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
MFPEFERMYD MANVEKKHFV DPAWPEHNPA DGHVVTELIS KVAGASSPWG DDKEFPVSAE ETGYVHPYTR INR

UniProtKB: Uncharacterized protein

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Macromolecule #12: Hypothetical membrane protein

MacromoleculeName: Hypothetical membrane protein / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 6.628905 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
MYMGKSFALL VLGAIILAGG VWYTIEVGYS VMAIVAALIM AAGGGIITWG LAVAADVNSP TSHKI

UniProtKB: Hypothetical membrane protein

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Macromolecule #13: Thiamine biosynthesis protein X

MacromoleculeName: Thiamine biosynthesis protein X / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 17.152379 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
CSPPHQQDSP VQRTNEILTT SQNPTSASST STSSATTTSS APVEEDVEIV VSPAALVDGE QVTFEISGLD PEGGYYAAIC DSVANPGNP VPSCTGEMAD FTSQAWLSNS QPGATVEIAE DGTATVELEA TATGTGLDCT TQACVAKVFG DHTEGFRDVA E VPVTFAAA

UniProtKB: Thiamine biosynthesis protein X

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Macromolecule #14: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 14 / 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 #15: [(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S...

MacromoleculeName: [(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3- ...Name: [(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate
type: ligand / ID: 15 / Number of copies: 2 / Formula: IZL
Molecular weightTheoretical: 1.677798 KDa
Chemical component information

ChemComp-IZL:
[(2~{R})-3-[[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{R})-10-methyldodecanoate

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Macromolecule #16: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3...

MacromoleculeName: (2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
type: ligand / ID: 16 / Number of copies: 4 / Formula: 9YF
Molecular weightTheoretical: 853.112 Da
Chemical component information

ChemComp-9YF:
(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate

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Macromolecule #17: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 17 / Number of copies: 6 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #18: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 18 / Number of copies: 10 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #19: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 19 / 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 #20: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 20 / Number of copies: 14 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #21: LYCOPENE

MacromoleculeName: LYCOPENE / type: ligand / ID: 21 / Number of copies: 2 / Formula: LYC
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-LYC:
LYCOPENE

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Macromolecule #22: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 22 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #23: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 23 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #24: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 24 / Number of copies: 2 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

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Macromolecule #25: HEME-AS

MacromoleculeName: HEME-AS / type: ligand / ID: 25 / Number of copies: 4 / Formula: HAS
Molecular weightTheoretical: 920.954 Da
Chemical component information

ChemComp-HAS:
HEME-AS

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Macromolecule #26: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 26 / Number of copies: 2 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #27: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 27 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #28: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 28 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #29: DINUCLEAR COPPER ION

MacromoleculeName: DINUCLEAR COPPER ION / type: ligand / ID: 29 / Number of copies: 4 / Formula: CUA
Molecular weightTheoretical: 127.092 Da
Chemical component information

ChemComp-CUA:
DINUCLEAR COPPER ION

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Macromolecule #30: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 30 / Number of copies: 6 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL

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Macromolecule #31: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 31 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #32: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S...

MacromoleculeName: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6- ...Name: [(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{S})-10-methylhenicosanoate
type: ligand / ID: 32 / Number of copies: 2 / Formula: IX7
Molecular weightTheoretical: 1.387749 KDa
Chemical component information

ChemComp-IX7:
[(2~{R})-3-[[(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{S})-10-methylhenicosanoate

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Macromolecule #33: water

MacromoleculeName: water / type: ligand / ID: 33 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3453 / Average electron dose: 49.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.3 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: 73863
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0)
Details: Reported by cisTEM, part-FSC using the 0.143 cut-off.
Number images used: 51060
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cisTEM (ver. 1.0.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM (ver. 1.0.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7qho:
Cytochrome bcc-aa3 supercomplex (respiratory supercomplex III2/IV2) from Corynebacterium glutamicum (as isolated)

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