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- EMDB-51689: Mycobacterial cytochrome bc1:aa3 with inhibitor -

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Basic information

Entry
Database: EMDB / ID: EMD-51689
TitleMycobacterial cytochrome bc1:aa3 with inhibitor
Map datamain map
Sample
  • Complex: cytochrome bc1:aa3
    • Protein or peptide: x 11 types
  • Ligand: x 14 types
Keywordsmembrane protein / inhibitor complex / mycobacterium / cytochrome bc / OXIDOREDUCTASE
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 / Uncharacterized protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
Authorslamers MH / Verma AK
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Innovative Medicines Initiative853903 Switzerland
Citation
Journal: NPJ Drug Discov / Year: 2025
Title: Structural and mechanistic study of a novel inhibitor analogue of cytochrome bc:aa.
Authors: Amit K Verma / Robbert Q Kim / Dirk A Lamprecht / Clara Aguilar-Pérez / Sarah Wong / Nicolas Veziris / Alexandra Aubry / José M Bartolomé-Nebreda / Rodrigo J Carbajo / Jennefer Wetzel / ...Authors: Amit K Verma / Robbert Q Kim / Dirk A Lamprecht / Clara Aguilar-Pérez / Sarah Wong / Nicolas Veziris / Alexandra Aubry / José M Bartolomé-Nebreda / Rodrigo J Carbajo / Jennefer Wetzel / Meindert H Lamers /
Abstract: Drug-resistant tuberculosis (TB) continues to challenge treatment options, necessitating the exploration of new compounds of novel targets. The mycobacterial respiratory complex cytochrome bc:aa has ...Drug-resistant tuberculosis (TB) continues to challenge treatment options, necessitating the exploration of new compounds of novel targets. The mycobacterial respiratory complex cytochrome bc:aa has emerged as a promising target, exemplified by the success of first-in-class inhibitor Q203 in phase 2 clinical trials. However, to fully exploit the potential of this target and to identify the best-in-class inhibitor more compounds need evaluation. Here, we introduce JNJ-2901, a novel Q203 analogue, that demonstrates activity against multidrug-resistant clinical strains at sub-nanomolar concentration and 4-log reduction in bacterial burden in a mouse model of TB infection. Inhibitory studies on purified enzymes validate the nanomolar inhibitions observed in mycobacterial cells. Additionally, cryo-EM structure analysis of cytochrome bc:aa bound to JNJ-2901 reveals the binding pocket at the menaquinol oxidation site (Qp), akin to other substate analogue inhibitors like Q203 and TB47. Validation of the binding site is further achieved by generating and isolating the JNJ-2901 resistant mutations in , followed by purification and resistance analysis of the resistant cytochrome bc:aa complex. Our comprehensive work lays the foundation for further clinical validations of JNJ-2901.
#1: Journal: Res Sq / Year: 2024
Title: Structural and mechanistic study of a novel inhibitor of M. tuberculosis cytochrome bc1:aa3
Authors: Lamers M / Verma A / Kim R / Lamprecht D / Perez CA / Wong S / Veziris N / Aubry A / Bartolome-Nebreda JM / Carbajo R / Wetzel J
History
DepositionOct 1, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51689.png

Downloads & links

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Map

FileDownload / File: emd_51689.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 420 pix.
= 351.12 Å		0.84 Å/pix.
x 420 pix.
= 351.12 Å		0.84 Å/pix.
x 420 pix.
= 351.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.03094605 - 0.06294489
Average (Standard dev.)0.00015191842 (±0.0016079493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 351.12003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap 1

Fileemd_51689_half_map_1.map
Annotationhalfmap 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap 2

Fileemd_51689_half_map_2.map
Annotationhalfmap 2
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : cytochrome bc1:aa3

EntireName: cytochrome bc1:aa3
Components
  • Complex: cytochrome bc1:aa3
    • 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: Transmembrane protein
    • Protein or peptide: Cytochrome c oxidase subunit 2
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome c oxidase polypeptide 4
    • Protein or peptide: Secreted protein
    • Protein or peptide: DUF5130 domain-containing protein
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
  • 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: PALMITIC ACID
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CARDIOLIPIN
  • Ligand: 6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide
  • Ligand: HEME C
  • Ligand: MENAQUINONE-9
  • Ligand: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
  • Ligand: COPPER (II) ION
  • Ligand: HEME-A
  • Ligand: CALCIUM ION
  • Ligand: MENAQUINONE-7
  • Ligand: water

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Supramolecule #1: cytochrome bc1:aa3

SupramoleculeName: cytochrome bc1:aa3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 667 KDa

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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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 46.383066 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MDYRNGGRHR CGHVDRIASM SQDSPDIKGT DAPGQTGVPG QPTDAELAEM SREELVKLGG KIDGVETIFK EPRWPVPGTK AEKRTERLV AYWLMLGGLS GLALLLVFLF WPWEYQPFGS EGEFLYSLAT PLYGLTFGLS ILSIGIGAVL FQKKFIPEEI S VQDRHDGR ...String:
MDYRNGGRHR CGHVDRIASM SQDSPDIKGT DAPGQTGVPG QPTDAELAEM SREELVKLGG KIDGVETIFK EPRWPVPGTK AEKRTERLV AYWLMLGGLS GLALLLVFLF WPWEYQPFGS EGEFLYSLAT PLYGLTFGLS ILSIGIGAVL FQKKFIPEEI S VQDRHDGR SPEVHRKTVA ANLTDALEGS TLKRRKVIGL SLGIGLGAFG AGTLVAFIGG LIKNPWKPVV PTAEGKKAVL WT SGWTPRF KGETIYLARA TGRPGESPFV KMRPEDIDAG GMETVFPWRE SDGDGTTVES EHKLTEIAMG VRNPVMLIRI KPA DMHRVI KRKGQESFNF GELFAYTKVC SHLGCPSSLY EQQTYRILCP CHQSQFDALE FAKPIFGPAA RALAQLPITI DEDG YLVAN GDFVEPVGPA FWERKS

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 / Details: mutations: F156Y, I182M, M189L, D309E, I312A / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 60.262934 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSPDFAKLAA AQGDAIDSRY HPSAAVRRQL NKVFPTHWSF LLGEIALYSF IILLLTGVWL TLFFDPSMAH VTYDGVYQPL RGVQMSRAY ETALDISFEV RGGLFVRQVH HWAALMFAAS IMVHLARIFF TGAFRRPREA NWVIGSLLLI LAMFEGYFGY S LPDDLLSG ...String:
MSPDFAKLAA AQGDAIDSRY HPSAAVRRQL NKVFPTHWSF LLGEIALYSF IILLLTGVWL TLFFDPSMAH VTYDGVYQPL RGVQMSRAY ETALDISFEV RGGLFVRQVH HWAALMFAAS IMVHLARIFF TGAFRRPREA NWVIGSLLLI LAMFEGYFGY S LPDDLLSG TGIRAALSGI TMGMPVIGTW LHWALFGGDF PGEILIPRLY ALHILLIPGI ILALIGAHLA LVWFQKHTQF PG PGRTETN VVGVRVMPVF AVKSGAFFAM ITGVLGLMGG LLTINPIWNL GPYKPSQVSA GSQPDFYMMW TEGLARLWPA 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 HH

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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 27.874547 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTSKSRRRLR RRLSAGLLLL IGLAVAGGVA ATLTPQPQVA VADESQSALL RTGKQLFETS CVSCHGANLQ GVPDRGPSLI GTGEAAVYF QVSTGRMPAM RGEAQAPSKP PHFDESQIDA LGAYVQANGG GPTVPRDDHG AVAQESLIGG DVARGGDLFR L NCASCHNF ...String:
MTSKSRRRLR RRLSAGLLLL IGLAVAGGVA ATLTPQPQVA VADESQSALL RTGKQLFETS CVSCHGANLQ GVPDRGPSLI GTGEAAVYF QVSTGRMPAM RGEAQAPSKP PHFDESQIDA LGAYVQANGG GPTVPRDDHG AVAQESLIGG DVARGGDLFR L NCASCHNF TGKGGALSSG KYAPDLGDAN PAQIYTAMLT GPQNMPKFSD RQLTPDEKRD IVAYVRESAE TPSYGGYGLG GF GPAPEGM AMWIIGMVAA IGVAMWIGSR A

UniProtKB: Cytochrome bc1 complex cytochrome c subunit

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Macromolecule #4: Transmembrane protein

MacromoleculeName: Transmembrane protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 9.531069 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
MANTEVERHT GVDVEDVPSA EWGWSHMPIG VMHIGGLLSA AFLLVMMRGN HVGHVEDWFL IGFAAVIVAL VGRNWWLRRR GWIR

UniProtKB: Transmembrane protein

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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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 38.077465 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (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 #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: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 64.162965 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (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 #7: Cytochrome c oxidase subunit 3

MacromoleculeName: Cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 22.196883 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (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 #8: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 15.177424 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (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 #9: Secreted protein

MacromoleculeName: Secreted protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 8.365549 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
MSTALTHGLI GGVPLVLFAV LALIFLTRKG PHPDTYKMSD PWTHAPILWA AEEPREHGHG GHGHDSHGVV IGGGASGKW

UniProtKB: Uncharacterized protein

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Macromolecule #10: DUF5130 domain-containing protein

MacromoleculeName: DUF5130 domain-containing protein / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 15.910971 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (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: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 23.232375 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (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 #12: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 12 / 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 #13: (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: 13 / 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 #14: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 14 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #15: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 15 / 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 #16: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 16 / Number of copies: 17 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #17: 6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro...

MacromoleculeName: 6-chloranyl-2-ethyl-N-[[4-[2-(trifluoromethylsulfonyl)-2-azaspiro[3.3]heptan-6-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide
type: ligand / ID: 17 / Number of copies: 2 / Formula: A1IRE
Molecular weightTheoretical: 540.986 Da

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Macromolecule #18: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 18 / Number of copies: 4 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #19: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 19 / Number of copies: 2 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #20: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)...

MacromoleculeName: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
type: ligand / ID: 20 / Number of copies: 4 / Formula: 9Y0
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-9Y0:
(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate

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Macromolecule #21: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 21 / Number of copies: 8 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #22: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 22 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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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: MENAQUINONE-7

MacromoleculeName: MENAQUINONE-7 / type: ligand / ID: 24 / Number of copies: 2 / Formula: MQ7
Molecular weightTheoretical: 648.999 Da
Chemical component information

ChemComp-MQ7:
MENAQUINONE-7

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Macromolecule #25: water

MacromoleculeName: water / type: ligand / ID: 25 / Number of copies: 211 / 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

Concentration3.3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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