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- EMDB-13777: III2-IV2 respiratory supercomplex from Corynebacterium glutamicum -

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Basic information

Entry
Database: EMDB / ID: EMD-13777
TitleIII2-IV2 respiratory supercomplex from Corynebacterium glutamicum
Map data
Sample
  • Complex: The respiratory supercomplex
    • Protein or peptide: x 14 types
  • Ligand: x 15 types
KeywordsMEMBRANE PROTEIN / CRYO-EM / RESPIRATORY SUPERCOMPLEX / ACTINOBACTERIA / ELECTRON TRANSPORT
Function / homology
Function and homology information


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 ...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) / 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) / 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 c / 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 / 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
Similarity search - Domain/homology
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 / Cytochrome c oxidase subunit 3
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria) / Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKovalova T / Moe A
Funding support Canada, 4 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Canada
Swedish Research Council Canada
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canada Research Chairs Canada
CitationJournal: Structure / Year: 2022
Title: The respiratory supercomplex from C. glutamicum.
Authors: Agnes Moe / Terezia Kovalova / Sylwia Król / David J Yanofsky / Michael Bott / Dan Sjöstrand / John L Rubinstein / Martin Högbom / Peter Brzezinski /
Abstract: Corynebacterium glutamicum is a preferentially aerobic gram-positive bacterium belonging to the phylum Actinobacteria, which also includes the pathogen Mycobacterium tuberculosis. In these bacteria, ...Corynebacterium glutamicum is a preferentially aerobic gram-positive bacterium belonging to the phylum Actinobacteria, which also includes the pathogen Mycobacterium tuberculosis. In these bacteria, respiratory complexes III and IV form a CIIICIV supercomplex that catalyzes oxidation of menaquinol and reduction of dioxygen to water. We isolated the C. glutamicum supercomplex and used cryo-EM to determine its structure at 2.9 Å resolution. The structure shows a central CIII dimer flanked by a CIV on two sides. A menaquinone is bound in each of the Q and Q sites in each CIII and an additional menaquinone is positioned ∼14 Å from heme b. A di-heme cyt. cc subunit electronically connects each CIII with an adjacent CIV, with the Rieske iron-sulfur protein positioned with the iron near heme b. Multiple subunits interact to form a convoluted sub-structure at the cytoplasmic side of the supercomplex, which defines a path for proton transfer into CIV.
History
DepositionOct 22, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.54
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.54
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7q21
  • Surface level: 0.54
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13777.png

Downloads & links

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Map

FileDownload / File: emd_13777.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 310 pix.
= 328.6 Å		1.06 Å/pix.
x 310 pix.
= 328.6 Å		1.06 Å/pix.
x 310 pix.
= 328.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.541 / Movie #1: 0.54
Minimum - Maximum-2.3948393 - 4.3314905
Average (Standard dev.)0.016408637 (±0.12276882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 328.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z310310310
origin x/y/z0.0000.0000.000
length x/y/z328.600328.600328.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS310310310
D min/max/mean-2.3954.3310.016

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Supplemental data

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Sample components

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Entire : The respiratory supercomplex

EntireName: The respiratory supercomplex
Components
  • Complex: The respiratory supercomplex
    • Protein or peptide: Co-purified unknown transmembrane helices built as polyALA (AscD)
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Uncharacterized membrane protein Cgl2017/cg2211
    • Protein or peptide: Cytochrome c oxidase polypeptide 4
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome bc1 complex Rieske iron-sulfur subunit
    • Protein or peptide: Uncharacterized protein Cgl2664/cg2949
    • Protein or peptide: Cytochrome bc1 complex cytochrome b subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: Co-purified unknown peptide built as polyALA (AscE)
    • Protein or peptide: Co-purified unknown peptide built as polyALA (AscE)
    • Protein or peptide: Actinobacterial supercomplex, subunit C (AscC)
    • Protein or peptide: Hypothetical membrane protein
  • Ligand: CARDIOLIPIN
  • Ligand: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
  • Ligand: TRIDECANE
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
  • Ligand: DOCOSANE
  • Ligand: COPPER (II) ION
  • Ligand: MAGNESIUM ION
  • Ligand: HEME-AS
  • Ligand: CALCIUM ION
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: MENAQUINONE-9
  • 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: PALMITIC ACID
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C

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Supramolecule #1: The respiratory supercomplex

SupramoleculeName: The respiratory supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)

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Macromolecule #1: Co-purified unknown transmembrane helices built as polyALA (AscD)

MacromoleculeName: Co-purified unknown transmembrane helices built as polyALA (AscD)
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 8.188084 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
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)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(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)(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)(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)(UNK)(UNK) (UNK)

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Macromolecule #2: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (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 #3: Uncharacterized membrane protein Cgl2017/cg2211

MacromoleculeName: Uncharacterized membrane protein Cgl2017/cg2211 / type: protein_or_peptide / ID: 3 / 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 #4: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (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 #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 (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 39.665562 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: MEQQNKRGLK RKALLGGVLG LGGLAMAGCE VAPPGGVLGD FLRMGWPDGI TPEAVAMGNF WSWVWVAAWI IGIIMWGLFL TAIFAWGAK RAEKRGEGEF PKQLQYNVPL ELVLTIVPII IVMVLFFFTV QTQDKVTALD KNPEVTVDVT AYQWNWKFGY S EIDGSLAP ...String:
MEQQNKRGLK RKALLGGVLG LGGLAMAGCE VAPPGGVLGD FLRMGWPDGI TPEAVAMGNF WSWVWVAAWI IGIIMWGLFL TAIFAWGAK RAEKRGEGEF PKQLQYNVPL ELVLTIVPII IVMVLFFFTV QTQDKVTALD KNPEVTVDVT AYQWNWKFGY S EIDGSLAP GGQDYQGSDP ERQAAAEASK KDPSGDNPIH GNSKSDVSYL EFNRIETLGT TDEIPVMVLP VNTPIEFNLA SA DVAHSFW VPEFLFKRDA YAHPEANKSQ RVFQIEEITE EGAFVGRCAE MCGTYHAMMN FELRVVDRDS FAEYISFRDS NPD ATNAQA LEHIGQAPYA TSTSPFVSDR TATRDGENTQ SNA

UniProtKB: Cytochrome c oxidase subunit 2

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Macromolecule #6: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (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 #7: Cytochrome bc1 complex Rieske iron-sulfur subunit

MacromoleculeName: Cytochrome bc1 complex Rieske iron-sulfur subunit / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (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 #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 (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025
Molecular weightTheoretical: 20.02575 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString: MEDESVKSLN LAARRGALVT VAAASALALA SCSAGQITQT SSQVAAVDGN QAGSANDPVL VRDVTVHLTT DGEAGVKFTA INQDTSHTS HTLESVTVDG EEVELDDAEP IERNCSLVAD IQSELDLIEE PEVGCIQHVA TSLENPGFAY GGVVPVEFVF D TGAITIDA ...String:
MEDESVKSLN LAARRGALVT VAAASALALA SCSAGQITQT SSQVAAVDGN QAGSANDPVL VRDVTVHLTT DGEAGVKFTA INQDTSHTS HTLESVTVDG EEVELDDAEP IERNCSLVAD IQSELDLIEE PEVGCIQHVA TSLENPGFAY GGVVPVEFVF D TGAITIDA TVSAPVLESG VENREVGGDT AEASHH

UniProtKB: Uncharacterized protein Cgl2664/cg2949

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Macromolecule #9: Cytochrome bc1 complex cytochrome b subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome b subunit / type: protein_or_peptide / ID: 9 / 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 #10: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (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 #11: Co-purified unknown peptide built as polyALA (AscE)

MacromoleculeName: Co-purified unknown peptide built as polyALA (AscE) / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 1.823254 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #12: Co-purified unknown peptide built as polyALA (AscE)

MacromoleculeName: Co-purified unknown peptide built as polyALA (AscE) / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum ATCC 13032 (bacteria)
Molecular weightTheoretical: 1.908359 KDa
Recombinant expressionOrganism: Corynebacterium glutamicum ATCC 13032 (bacteria)
SequenceString:
C(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #13: Actinobacterial supercomplex, subunit C (AscC)

MacromoleculeName: Actinobacterial supercomplex, subunit C (AscC) / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (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 #14: Hypothetical membrane protein

MacromoleculeName: Hypothetical membrane protein / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025) (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 #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 14 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #16: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate

MacromoleculeName: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
type: ligand / ID: 16 / Number of copies: 16 / Formula: 7PH
Molecular weightTheoretical: 564.732 Da
Chemical component information

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

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Macromolecule #17: TRIDECANE

MacromoleculeName: TRIDECANE / type: ligand / ID: 17 / Number of copies: 18 / Formula: TRD
Molecular weightTheoretical: 184.361 Da
Chemical component information

ChemComp-TRD:
TRIDECANE

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Macromolecule #18: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
type: ligand / ID: 18 / Number of copies: 4 / Formula: 9XX
Molecular weightTheoretical: 594.992 Da
Chemical component information

ChemComp-9XX:
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

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Macromolecule #19: DOCOSANE

MacromoleculeName: DOCOSANE / type: ligand / ID: 19 / Number of copies: 2 / Formula: TWT
Molecular weightTheoretical: 310.601 Da
Chemical component information

ChemComp-TWT:
DOCOSANE

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Macromolecule #20: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 20 / Number of copies: 6 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #21: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 21 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #22: HEME-AS

MacromoleculeName: HEME-AS / type: ligand / ID: 22 / Number of copies: 4 / Formula: HAS
Molecular weightTheoretical: 920.954 Da
Chemical component information

ChemComp-HAS:
HEME-AS

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Macromolecule #23: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 23 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #24: FE2/S2 (INORGANIC) CLUSTER

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

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #25: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 25 / Number of copies: 6 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #26: (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: 26 / 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 #27: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 27 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #28: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 28 / 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 #29: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 29 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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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: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 276 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65391
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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