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- EMDB-50752: CIII2/CIV respiratory supercomplex from Mycobacterium smegmatis w... -

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Basic information

Entry
Database: EMDB / ID: EMD-50752
TitleCIII2/CIV respiratory supercomplex from Mycobacterium smegmatis with lansoprazole sulfide
Map data
Sample
  • Complex: The respiratory supercomplex
    • Protein or peptide: x 12 types
  • Ligand: x 19 types
KeywordsRESPIRATORY SUPERCOMPLEX / MEMBRANE PROTEIN / 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 / superoxide dismutase / electron transport coupled proton transport / superoxide dismutase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ...aerobic electron transport chain / cytochrome-c oxidase / oxidative phosphorylation / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / superoxide dismutase / electron transport coupled proton transport / superoxide dismutase activity / 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) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / 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 ...Protein of unknown function DUF2631 / Protein of unknown function (DUF2631) / Protein of unknown function DUF5130 / Domain of unknown function (DUF5130) / 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 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 / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / 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 II, periplasmic domain / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / 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 / Rieske iron-sulphur protein / Cytochrome c / 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
Cytochrome c oxidase subunit 1 / Superoxide dismutase [Cu-Zn] / Transmembrane protein / Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Uncharacterized protein MSMEG_4692/MSMEI_4575 ...Cytochrome c oxidase subunit 1 / Superoxide dismutase [Cu-Zn] / Transmembrane protein / Probable cytochrome c oxidase subunit 3 / Cytochrome bc1 complex cytochrome c subunit / Cytochrome bc1 complex Rieske iron-sulfur subunit / Cytochrome bc1 complex cytochrome b subunit / Cytochrome c oxidase polypeptide 4 / cytochrome-c oxidase / Uncharacterized protein MSMEG_4692/MSMEI_4575 / Uncharacterized protein / LpqE protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsKovalova T / Krol S / Gamiz-Hernandez A / Sjostrand D / Kaila V / Brzezinski P / Hogbom M
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2019.0043 Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide.
Authors: Terezia Kovalova / Sylwia Król / Ana P Gamiz-Hernandez / Dan Sjöstrand / Ville R I Kaila / Peter Brzezinski / Martin Högbom /
Abstract: Tuberculosis is one of the most common causes of death worldwide, with a rapid emergence of multi-drug-resistant strains underscoring the need for new antituberculosis drugs. Recent studies indicate ...Tuberculosis is one of the most common causes of death worldwide, with a rapid emergence of multi-drug-resistant strains underscoring the need for new antituberculosis drugs. Recent studies indicate that lansoprazole-a known gastric proton pump inhibitor and its intracellular metabolite, lansoprazole sulfide (LPZS)-are potential antituberculosis compounds. Yet, their inhibitory mechanism and site of action still remain unknown. Here, we combine biochemical, computational, and structural approaches to probe the interaction of LPZS with the respiratory chain supercomplex IIIIV of , a close homolog of supercomplex. We show that LPZS binds to the Q cavity of the mycobacterial supercomplex, inhibiting the quinol substrate oxidation process and the activity of the enzyme. We solve high-resolution (2.6 Å) cryo-electron microscopy (cryo-EM) structures of the supercomplex with bound LPZS that together with microsecond molecular dynamics simulations, directed mutagenesis, and functional assays reveal key interactions that stabilize the inhibitor, but also how mutations can lead to the emergence of drug resistance. Our combined findings reveal an inhibitory mechanism of LPZS and provide a structural basis for drug development against tuberculosis.
History
DepositionJun 25, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50752.png

Downloads & links

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Map

FileDownload / File: emd_50752.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 540 pix.
= 447.12 Å		0.83 Å/pix.
x 540 pix.
= 447.12 Å		0.83 Å/pix.
x 540 pix.
= 447.12 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.176
Minimum - Maximum-0.6281697 - 1.165533
Average (Standard dev.)-0.00024766402 (±0.032719005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 447.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50752_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_50752_half_map_2.map
Projections & Slices
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Histogram (log scale)

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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: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: Cytochrome bc1 complex cytochrome b subunit
    • Protein or peptide: Transmembrane protein
    • Protein or peptide: Probable cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase polypeptide 4
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: cytochrome-c oxidase
    • Protein or peptide: Cytochrome c oxidase subunit
    • Protein or peptide: Uncharacterized protein MSMEG_4692/MSMEI_4575
    • Protein or peptide: LpqE protein
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
  • Ligand: MENAQUINONE-9
  • Ligand: acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)
  • Ligand: HEME C
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • 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: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
  • 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: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARDIOLIPIN
  • Ligand: Lansoprazole sulfide
  • Ligand: TRIDECANE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: CALCIUM ION
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
  • Ligand: MAGNESIUM ION
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: The respiratory supercomplex

SupramoleculeName: The respiratory supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

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Macromolecule #1: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 29.109945 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MHHHHHHMGS MTSKSRRRLR RRLSAGLLLL IGLAVAGGVA ATLTPQPQVA VADESQSALL RTGKQLFETS CVSCHGANLQ GVPDRGPSL IGTGEAAVYF QVSTGRMPAM RGEAQAPSKP PHFDESQIDA LGAYVQANGG GPTVPRDDHG AVAQESLIGG D VARGGDLF ...String:
MHHHHHHMGS MTSKSRRRLR RRLSAGLLLL IGLAVAGGVA ATLTPQPQVA VADESQSALL RTGKQLFETS CVSCHGANLQ GVPDRGPSL IGTGEAAVYF QVSTGRMPAM RGEAQAPSKP PHFDESQIDA LGAYVQANGG GPTVPRDDHG AVAQESLIGG D VARGGDLF RLNCASCHNF TGKGGALSSG KYAPDLGDAN PAQIYTAMLT GPQNMPKFSD RQLTPDEKRD IVAYVRESAE TP SYGGYGL GGFGPAPEGM AMWIIGMVAA IGVAMWIGSR A

UniProtKB: Cytochrome bc1 complex cytochrome c subunit

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Macromolecule #2: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 44.869395 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MDRIASMSQD SPDIKGTDAP GQTGVPGQPT DAELAEMSRE ELVKLGGKID GVETIFKEPR WPVPGTKAEK RTERLVAYWL MLGGLSGLA LLLVFLFWPW EYQPFGSEGE FLYSLATPLY GLTFGLSILS IGIGAVLFQK KFIPEEISVQ DRHDGRSPEV H RKTVAANL ...String:
MDRIASMSQD SPDIKGTDAP GQTGVPGQPT DAELAEMSRE ELVKLGGKID GVETIFKEPR WPVPGTKAEK RTERLVAYWL MLGGLSGLA LLLVFLFWPW EYQPFGSEGE FLYSLATPLY GLTFGLSILS IGIGAVLFQK KFIPEEISVQ DRHDGRSPEV H RKTVAANL TDALEGSTLK RRKVIGLSLG IGLGAFGAGT LVAFIGGLIK NPWKPVVPTA EGKKAVLWTS GWTPRFKGET IY LARATGR PGESPFVKMR PEDIDAGGME TVFPWRESDG DGTTVESEHK LTEIAMGVRN PVMLIRIKPA DMHRVIKRKG QES FNFGEL FAYTKVCSHL GCPSSLYEQQ TYRILCPCHQ SQFDALEFAK PIFGPAARAL AQLPITIDED GYLVANGDFV EPVG PAFWE RKS

UniProtKB: Cytochrome bc1 complex Rieske iron-sulfur subunit

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Macromolecule #3: Cytochrome bc1 complex cytochrome b subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome b subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 61.514281 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MSPDFAKLAA AQGDAIDSRY HPSAAVRRQL NKVFPTHWSF LLGEIALYSF IILLLTGVWL TLFFDPSMAH VTYDGVYQPL RGVQMSRAY ETALDISFEV RGGLFVRQVH HWAALMFAAS IMVHLARIFF TGAFRRPREA NWVIGSLLLI LAMFEGFFGY S LPDDLLSG ...String:
MSPDFAKLAA AQGDAIDSRY HPSAAVRRQL NKVFPTHWSF LLGEIALYSF IILLLTGVWL TLFFDPSMAH VTYDGVYQPL RGVQMSRAY ETALDISFEV RGGLFVRQVH HWAALMFAAS IMVHLARIFF TGAFRRPREA NWVIGSLLLI LAMFEGFFGY S LPDDLLSG TGIRAALSGI TMGIPVIGTW MHWALFGGDF PGEILIPRLY ALHILLIPGI ILALIGAHLA LVWFQKHTQF PG PGRTETN VVGVRVMPVF AVKSGAFFAM ITGVLGLMGG LLTINPIWNL GPYKPSQVSA GSQPDFYMMW TDGLIRLWPA WEF YPFGHT IPQGVWVAVG MGLVFALLIA YPFIEKKVTG DDAHHNLLQR PRDVPVRTAI GSMAIALYLL LTFACMNDII ALKF HISLN ATTWIGRIGM VVLPAIVYFV AYRWAISLQR SDREVLEHGV ETGIIKRLPH GAYVELHQPL GPVDEHGHPI PLEYA GAPL PKRMNKLGSG GAPGTGSFLF PDPAVEHEAL TEAAHASEHK SLTALKEHQD RIHGNGETNG HHKLDYKDDD DK

UniProtKB: Cytochrome bc1 complex cytochrome b subunit

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Macromolecule #4: Transmembrane protein

MacromoleculeName: Transmembrane protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 11.329909 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MSSTQDRSQL DPEEQPVANT EVERHTGVDV EDVPSAEWGW SHMPIGVMHI GGLLSAAFLL VMMRGNHVGH VEDWFLIGFA AVIVALVGR NWWLRRRGWI R

UniProtKB: Transmembrane protein

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Macromolecule #5: Probable cytochrome c oxidase subunit 3

MacromoleculeName: Probable cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 22.196883 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTSAVGTSGT AITSRVHSLN RPNMVSVGTI VWLSSELMFF AGLFAMYFTA RAQAGGAWPP EPTELNLALA VPVTLVLIAS SFTCQMGVF AAERGDVFGL RRWYVITFLM GLFFVLGQGY EYIHLVEHGT TIPGSAYGSV FYLATGFHGL HVIGGLVAFV L LLARTKMS ...String:
MTSAVGTSGT AITSRVHSLN RPNMVSVGTI VWLSSELMFF AGLFAMYFTA RAQAGGAWPP EPTELNLALA VPVTLVLIAS SFTCQMGVF AAERGDVFGL RRWYVITFLM GLFFVLGQGY EYIHLVEHGT TIPGSAYGSV FYLATGFHGL HVIGGLVAFV L LLARTKMS KFTPAQATAA IVVSYYWHFV DIVWIALFAT IYFVR

UniProtKB: Probable cytochrome c oxidase subunit 3

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Macromolecule #6: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 15.177424 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MHIEARLFEI LTAFFALAAV VYAVLTAMFA TGGVEWAGTT ALVLTTGLTL ITGTFFRFVA RRLDTRPEDY EDAEISDGAG ELGFFAPHS WWPILISLSF STAAVGAALW LPWLIAAGVA FVITSVCGLV FEYYWGPEKH

UniProtKB: Cytochrome c oxidase polypeptide 4

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Macromolecule #7: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 64.162965 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MVAEAPPIGE LEARRPFPER MGPKGNLIYK LITTTDHKLI GIMYCVVCFA FFLVGGLMAL FMRTELAMPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANLVLPL QIGAPDVAFP RLNALSFWLF LFGALIAIAG FITPGGAADF GWTAYSPLTD A IHSPGAGG ...String:
MVAEAPPIGE LEARRPFPER MGPKGNLIYK LITTTDHKLI GIMYCVVCFA FFLVGGLMAL FMRTELAMPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANLVLPL QIGAPDVAFP RLNALSFWLF LFGALIAIAG FITPGGAADF GWTAYSPLTD A IHSPGAGG DLWIMGLAVG GLGTILGGVN MITTVVCMRA PGMTMFRMPI FTWNILVTSI LVLIAFPILT AALFGLAADR HL GAHIYDP ANGGVLLWQH LFWFFGHPEV YIIALPFFGI VSEIFPVFSR KPIFGYTTLI YATLAIAALS VAVWAHHMYA TGA VLLPFF SFMTFLIAVP TGIKFFNWIG TMWKGQLTFE TPMLFSVGFL ITFLLGGLSG VLLASPPLDF HVTDSYFVIA HFHY VLFGT IVFATYAGIY FWFPKMTGRL LDERLGKLHF WLTFIGFHTT FLVQHWLGDE GMPRRYADYL PTDGFTTLNV ISTVG AFIL GVSMLPFVWN VFKSWRYGEP VTVDDPWGYG NSLEWATSCP PPRHNFTELP RIRSERPAFE LHYPHMVERM RAEAHV GRA HHPELETADK SS

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #8: cytochrome-c oxidase

MacromoleculeName: cytochrome-c oxidase / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 38.077465 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MTPRGFRVVA LSIVLGGSAL LLSGCSWSDA LALGWPTGIT PEAKLNRELW IGSVIASFAV GAIVWGLIFW TSAFHRKKAT DTELPRQFG YNMPLELTLT VIPFLIISVL FYFTVVVQER MMHKDPNPEV VIDVTAFQWN WKFGYQKIAF ADGSFDYDGA D PERKEAMT ...String:
MTPRGFRVVA LSIVLGGSAL LLSGCSWSDA LALGWPTGIT PEAKLNRELW IGSVIASFAV GAIVWGLIFW TSAFHRKKAT DTELPRQFG YNMPLELTLT VIPFLIISVL FYFTVVVQER MMHKDPNPEV VIDVTAFQWN WKFGYQKIAF ADGSFDYDGA D PERKEAMT SRPEGKDEHG IEKVGPIRGM TPEDRTYLNF DKIETLGTSS EIPVLVLPAG KRIEFVLNSA DVIHGFWVPE FL FKRDVLP EPKANNSDNV FQVSEIQQTG AFVGRCTEMC GTFHAMMNFE VRVVEPNDFK AYIDQRNAGK TNAEALAAIN QPP LAITTE PFESRRGELV PQASK

UniProtKB: cytochrome-c oxidase

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Macromolecule #9: Cytochrome c oxidase subunit

MacromoleculeName: Cytochrome c oxidase subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 8.365549 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MSTALTHGLI GGVPLVLFAV LALIFLTRKG PHPDTYKMSD PWTHAPILWA AEEPREHGHG GHGHDSHGVV IGGGASGKW

UniProtKB: Uncharacterized protein

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Macromolecule #10: Uncharacterized protein MSMEG_4692/MSMEI_4575

MacromoleculeName: Uncharacterized protein MSMEG_4692/MSMEI_4575 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 15.910971 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MASGDIATVA NAELDLPYGS ALTSSGRISA VTEPGELSVH YPFPTMDLVV LDDALKYGSR AAKARFAVYI GPLGADTAAT AREILANVP TPENAVLLAV SPDQRAIEVV YGADVKGRGI ESAAPLGVSA AAASFKEGNL IDGLISAVRV MSAGVSPA

UniProtKB: Uncharacterized protein MSMEG_4692/MSMEI_4575

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Macromolecule #11: LpqE protein

MacromoleculeName: LpqE protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 19.118969 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString:
MNRFSSRAGL AVCGLATAVA LTACSAGQIS QTTTQEPAVN GVNAQAGQVS LRNVHLRAPQ QTDYVEPGTT VELLFVAAND STEGSNKLK SITSDVGEVT LTGDSTVPAD GVLIVGEPDG QIQAVENAEA ADAVTAEVEL TKPITNGLLY DFTFTFEDGE T TVAVPISA GEQPRRPVPP AGPGSSEH

UniProtKB: LpqE protein

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Macromolecule #12: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 23.232375 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MLKPVSVAVL FATPVLALSA CSPPGETASS EPGTTPAIWT GSPSPAAPSG EDHGGGHGAG AAGAGETLTA ELKTADGTSV ATADFQFAD GFATVTIETT TPGRLTPGFH GVHIHSVGKC EANSVAPTGG APGDFNSAGG HFQVSGHSGH PASGDLSSLQ V RADGSGKL ...String:
MLKPVSVAVL FATPVLALSA CSPPGETASS EPGTTPAIWT GSPSPAAPSG EDHGGGHGAG AAGAGETLTA ELKTADGTSV ATADFQFAD GFATVTIETT TPGRLTPGFH GVHIHSVGKC EANSVAPTGG APGDFNSAGG HFQVSGHSGH PASGDLSSLQ V RADGSGKL VTTTDAFTAE DLLDGAKTAI IIHEKADNFA NIPPERYQQV NGAPGPDQTT MATGDAGSRV ACGVISAG

UniProtKB: Superoxide dismutase [Cu-Zn]

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Macromolecule #13: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 13 / Number of copies: 5 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #14: acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2)

MacromoleculeName: acyl-phosphatidyl-myo-inositol dimannoside (AcPIM2) / type: ligand / ID: 14 / Number of copies: 2 / Formula: WUO
Molecular weightTheoretical: 1.415802 KDa

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Macromolecule #15: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 15 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #16: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 16 / 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 #17: (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: 17 / Number of copies: 3 / 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 #18: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate

MacromoleculeName: (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
type: ligand / ID: 18 / Number of copies: 4 / 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 #19: [(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: 19 / 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 #20: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 20 / 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 #21: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 21 / Number of copies: 9 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #22: Lansoprazole sulfide

MacromoleculeName: Lansoprazole sulfide / type: ligand / ID: 22 / Number of copies: 1 / Formula: A1IGA
Molecular weightTheoretical: 353.362 Da

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Macromolecule #23: TRIDECANE

MacromoleculeName: TRIDECANE / type: ligand / ID: 23 / Number of copies: 5 / Formula: TRD
Molecular weightTheoretical: 184.361 Da
Chemical component information

ChemComp-TRD:
TRIDECANE

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Macromolecule #24: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 24 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

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

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Macromolecule #25: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 25 / Number of copies: 2 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #26: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 26 / Number of copies: 3 / 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: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #28: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
type: ligand / ID: 28 / Number of copies: 3 / 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 #29: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 29 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #30: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 30 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #31: water

MacromoleculeName: water / type: ligand / ID: 31 / Number of copies: 348 / 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

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100396
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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