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- EMDB-65878: Cryo-EM structure of the Mycobacterium abscessus cytochrome bcc:a... -

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Basic information

Entry
Database: EMDB / ID: EMD-65878
TitleCryo-EM structure of the Mycobacterium abscessus cytochrome bcc:aa3 supercomplex
Map data
Sample
  • Complex: Mycobacterium abscessus cytochrome bcc:aa3 supercomplex
    • Protein or peptide: x 12 types
  • Ligand: x 13 types
KeywordsApo structure of Supercomplex / OXIDOREDUCTASE
Biological speciesMycobacteroides abscessus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsMathiyazakan V / Gruber G
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-CRP27-2021-0002 Singapore
CitationJournal: Nat Commun / Year: 2026
Title: The Mycobacterium abscessus cytochrome bcc:aa oxidase structure paves the way for an agent targeting subunit QcrB.
Authors: Vikneswaran Mathiyazakan / Emilia Xin Yi Tan / Garrett Moraski / Sandip Basak / Wuan-Geok Saw / Kevin Pethe / Gerhard Grüber /
Abstract: The cytochrome bcc:aa oxidase is the target of telacebec, a clinically advanced drug developed for Mycobacterium tuberculosis. However, telacebec is inactive against Mycobacterium abscessus, an ...The cytochrome bcc:aa oxidase is the target of telacebec, a clinically advanced drug developed for Mycobacterium tuberculosis. However, telacebec is inactive against Mycobacterium abscessus, an opportunistic pathogen increasingly linked to chronic pulmonary infections and notoriously known for intrinsic resistance to numerous antibiotics. Here, we report the 2.6 Å cryo-electron microscopy structure of the M. abscessus bcc:aa cytochrome oxidase supercomplex, revealing key pathways and the evolution of the mycobacterial QcrB menaquinol-binding cavity. Structure-guided mutagenesis identified polymorphisms that modulate telacebec binding and potency in both M. abscessus and Mycobacterium smegmatis. Leveraging these insights, we designed ND-011458, a QcrB inhibitor with potent activity against M. abscessus and being bactericidal in combination with Clofazimine. The 2.26 Å inhibitor-bound structure elucidates its binding mode and provides a framework for the design of next-generation inhibitors for M. abscessus pulmonary diseases.
History
DepositionAug 18, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65878.png

Downloads & links

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Map

FileDownload / File: emd_65878.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 600 pix.
= 402.6 Å		0.67 Å/pix.
x 600 pix.
= 402.6 Å		0.67 Å/pix.
x 600 pix.
= 402.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.671 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-1.7074511 - 3.8179588
Average (Standard dev.)0.0007349326 (±0.07221767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 402.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65878_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_65878_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mycobacterium abscessus cytochrome bcc:aa3 supercomplex

EntireName: Mycobacterium abscessus cytochrome bcc:aa3 supercomplex
Components
  • Complex: Mycobacterium abscessus cytochrome bcc:aa3 supercomplex
    • Protein or peptide: Prokaryotic respiratory supercomplex associate factor 1
    • Protein or peptide: Cytochrome c oxidase subunit 1
    • Protein or peptide: Cytochrome c oxidase subunit CtaJ
    • Protein or peptide: Cytochrome bc1 complex cytochrome c subunit
    • Protein or peptide: Cytochrome bc1 complex Rieske iron-sulfur subunit
    • Protein or peptide: Superoxide dismutase [Cu-Zn]
    • Protein or peptide: cytochrome-c oxidase
    • Protein or peptide: Probable cytochrome c oxidase subunit 3
    • Protein or peptide: Cytochrome bc1 complex cytochrome b subunit
    • Protein or peptide: DUF5130 domain-containing protein
    • Protein or peptide: Cytochrome c oxidase polypeptide 4
    • Protein or peptide: Lipoprotein lpqE
  • Ligand: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
  • Ligand: CARDIOLIPIN
  • Ligand: (2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
  • Ligand: HEME-A
  • Ligand: COPPER (II) ION
  • Ligand: PALMITIC ACID
  • Ligand: OXYGEN MOLECULE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • 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: MENAQUINONE-9
  • Ligand: HEME C
  • Ligand: water

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Supramolecule #1: Mycobacterium abscessus cytochrome bcc:aa3 supercomplex

SupramoleculeName: Mycobacterium abscessus cytochrome bcc:aa3 supercomplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 760 kDa/nm

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Macromolecule #1: Prokaryotic respiratory supercomplex associate factor 1

MacromoleculeName: Prokaryotic respiratory supercomplex associate factor 1
type: protein_or_peptide / ID: 1 / Details: A0A1U1LTV7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 10.679506 KDa
SequenceString:
MACSRRLRFG GLAVATTEVV KYDGVDVEDV PSVAFGRGLS GQNPRVFHVL GVVMAAILLL MLIGNHVGKV EDIFLVGFAA IVLAFTAND YFGRRSGRIR

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Macromolecule #2: Cytochrome c oxidase subunit 1

MacromoleculeName: Cytochrome c oxidase subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 62.69216 KDa
SequenceString: MTAEAPPIGG LQASRPFPPR MGARGTLIYR LITTTDHKLI GIMYLVACFA FFLIGGLMAL FMRAELAVPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANVVLPL QIGAPDVAFP RLNAFSFWLF LFGALIGIAG FITPGGAADF GWTAYTPLTD A IHSPGAGA ...String:
MTAEAPPIGG LQASRPFPPR MGARGTLIYR LITTTDHKLI GIMYLVACFA FFLIGGLMAL FMRAELAVPG LQFLSNEQFN QLFTMHGTV MLLFYATPIV FGFANVVLPL QIGAPDVAFP RLNAFSFWLF LFGALIGIAG FITPGGAADF GWTAYTPLTD A IHSPGAGA DLWIMGLAVG GLGTILGAVN MITTVVCMRA PGMTMFRMPI FTWNILVTSV LVLLAFPLLT AALFGLAADR HL GAHVFDP ANGGVLLWQH LFWFFGHPEV YIIALPFFGI VSEIFPVFSR KPIFGYTTLI YATLGIAALS IAVWAHHMYA TGA VLLPFF SFMTFLIAVP TGIKFFNWIG TMWKGQLTFE TPMIFSVGFL VTFLFGGLTG VLLAMPPVDF HVTDSYFVIA HFHY VLFGT IVFATYAGIY FWFPKMTGRL LDERLGKFHF WLTFIGFHST FLVQHWLGNQ GMPRRYADYL PTDGFTFLNS FSTVG AFIL GASTLPFLWN VFKSYRYGEV VTVDDPWGYG NSLEWATSCP PPRHNFSELP RIRSERPAFE LHYPHMSERM RAEAHV GGG H

UniProtKB: Cytochrome c oxidase subunit 1

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Macromolecule #3: Cytochrome c oxidase subunit CtaJ

MacromoleculeName: Cytochrome c oxidase subunit CtaJ / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 9.157419 KDa
SequenceString:
MSFLNSPTYI GMPVWVALIT PVAFVLIGLW TMRKKGPHPA TYNMNDGWTH GPILWAAVDE NIGDAHGHGH GHAGAEAIGG SASGKW

UniProtKB: Uncharacterized protein

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Macromolecule #4: Cytochrome bc1 complex cytochrome c subunit

MacromoleculeName: Cytochrome bc1 complex cytochrome c subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 31.176285 KDa
SequenceString: MPDGPKTQPS PVKGAQQVSV EPVKDTAAKN RARRKFRRRV SAGLLLLIAL VVAGGLASTF TPTPQVAVAD EDKSALLRTG KQLYETSCI TCHGANLQGV PDRGPSLIGV GEAAVYFQVS TGRMPAMRNE AQAQRKDPIF DEEQTDALGA YIQANGGGPQ V IRDRDGAV ...String:
MPDGPKTQPS PVKGAQQVSV EPVKDTAAKN RARRKFRRRV SAGLLLLIAL VVAGGLASTF TPTPQVAVAD EDKSALLRTG KQLYETSCI TCHGANLQGV PDRGPSLIGV GEAAVYFQVS TGRMPAMRNE AQAQRKDPIF DEEQTDALGA YIQANGGGPQ V IRDRDGAV AQESLRGNNI ARGGDLFRLN CASCHNFTGR GGALSSGKFA PELDPATEQQ IYTAMLTGPQ NMPKFSDRQL TV DEKKDII AYVRASSETP DPGGYGLGGF GPTSEGMAMW IIGIVAAIAA ALWIGARA

UniProtKB: Cytochrome bc1 complex cytochrome c subunit

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Macromolecule #5: Cytochrome bc1 complex Rieske iron-sulfur subunit

MacromoleculeName: Cytochrome bc1 complex Rieske iron-sulfur subunit / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 43.008285 KDa
SequenceString: MSVSDADKPE IPSDEQLAAM SRDELVKLGT NLDGVEIVYR EPRWPVEGTK AEKRAERLVA LWFALGGVFG LALLGVFLFW PWEYKPFGD PGNALYNLAT PLYGLTLGLS VLSLGIGAVL YTKKFIPQEI SIQDRHDGPG SAEVDRKTIV AQLQDTLDTS T LPRRKMIV ...String:
MSVSDADKPE IPSDEQLAAM SRDELVKLGT NLDGVEIVYR EPRWPVEGTK AEKRAERLVA LWFALGGVFG LALLGVFLFW PWEYKPFGD PGNALYNLAT PLYGLTLGLS VLSLGIGAVL YTKKFIPQEI SIQDRHDGPG SAEVDRKTIV AQLQDTLDTS T LPRRKMIV RALGFGVGAM GAGTAVAFIG GMIKNPWARV VPTANGKQPV LLTSGWTPRY HGETIYLGRA VGSSSNVLLK IR PEDIDAG GMETVFPWRE SDGDGTTVES HEKLSHIQMG IRNPVMLIRV RPTDMPKVVK RKGQENFNYG DLFAYTKICS HLG CPTSLF EQQTYRILCP CHQSQFDALH FAKPIFGPAA RALAQLPLTV DKDGYLVANG DFVEPVGPAF WERKS

UniProtKB: Cytochrome bc1 complex Rieske iron-sulfur subunit

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Macromolecule #6: Superoxide dismutase [Cu-Zn]

MacromoleculeName: Superoxide dismutase [Cu-Zn] / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: superoxide dismutase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 23.842414 KDa
SequenceString: MKPMVKPAVL ASGTLAAVAL SLSGCSPDQQ ASTTPGTTPP VWTGSTAPAT AGEHGGHGGG EQPVPAGEKL NATLKLADGT PVATAAFVF QDGYARITVK TTQNGKLTPG FHGLHIHSFK KCEANSVAPA GGAPGDFLSA GGHFNVPGYT GHPSSGDLVS L NILKDGSG ...String:
MKPMVKPAVL ASGTLAAVAL SLSGCSPDQQ ASTTPGTTPP VWTGSTAPAT AGEHGGHGGG EQPVPAGEKL NATLKLADGT PVATAAFVF QDGYARITVK TTQNGKLTPG FHGLHIHSFK KCEANSVAPA GGAPGDFLSA GGHFNVPGYT GHPSSGDLVS L NILKDGSG ELVTTADSFT KEDLLAGNGT AIIIHEKSDN FANIPAERYT QANGASGPDD TTKSTGDAGK RVACGLIDAG

UniProtKB: Superoxide dismutase [Cu-Zn]

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Macromolecule #7: cytochrome-c oxidase

MacromoleculeName: cytochrome-c oxidase / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 38.750297 KDa
SequenceString: MTSRSGSRPS LLATVVLLGA ASFLLSGCSV QEVLRFGWPE GITPEAHDYM APLWTWAVVA SLVVGVIVWG LTFWTVAFHR HKPGDTEFP RQFGYNLPLE LVLTVVPFLI IAVLFYFTVV VQNKVMHKDP NPEVVVDVTA FQWNWKFGYQ KVAFKDGSLN Y EGADPERK ...String:
MTSRSGSRPS LLATVVLLGA ASFLLSGCSV QEVLRFGWPE GITPEAHDYM APLWTWAVVA SLVVGVIVWG LTFWTVAFHR HKPGDTEFP RQFGYNLPLE LVLTVVPFLI IAVLFYFTVV VQNKVMHKDP NPEVVVDVTA FQWNWKFGYQ KVAFKDGSLN Y EGADPERK KAMTSKPEGK DAHGNELVGP VRGLNREDRT YLNFDKIETV GTSSEIPVLV VPSGKSIEFQ LASADVIHSF RV VPFLFTR DVMPEPKANN SDNVFQVSKI LKEGAFVGRC VEMCGTYHSM MAFELRVVSP NDFKFYLKAR QDGKSNAEAL ASI GQSPVS ITTRPFDGRR GDLAPVDNNA AKN

UniProtKB: cytochrome-c oxidase

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Macromolecule #8: Probable cytochrome c oxidase subunit 3

MacromoleculeName: Probable cytochrome c oxidase subunit 3 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 22.538057 KDa
SequenceString: MTTAAAPGSP AGTAITQRVH SLNRPNMVSV GTIVWLSSEL MFFAGLFAFY FTARAQSGGN WPPEPTELNL GLAIPVTAVL VASSFTCQM GVFAAERGDV FGLRRWYVIT LIMGTFFVLG QGYEYMNLVH EGTTIAGSAY GSTFYLATGF HGLHVIGGLV A FVYLLIRT ...String:
MTTAAAPGSP AGTAITQRVH SLNRPNMVSV GTIVWLSSEL MFFAGLFAFY FTARAQSGGN WPPEPTELNL GLAIPVTAVL VASSFTCQM GVFAAERGDV FGLRRWYVIT LIMGTFFVLG QGYEYMNLVH EGTTIAGSAY GSTFYLATGF HGLHVIGGLV A FVYLLIRT RMSKFTPAQA TSAIVVSYYW HFVDIVWIAL FATIYFVR

UniProtKB: Probable cytochrome c oxidase subunit 3

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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: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 60.461324 KDa
SequenceString: MSDTAQKPSR AAKQAEAMDS RYHLAAGMKR QINKVFPTHW SFMLGEIALY SFIVLLLSGV YLTLFFDPSM SEVTYNGIYQ PLRGVQMSK AYETTLNISF EVRGGLFVRQ IHHWAALMFA ASIMVHMARI FFTGAFRRPR EANWVIGALL FILAMFEGFF G YSLPDDLL ...String:
MSDTAQKPSR AAKQAEAMDS RYHLAAGMKR QINKVFPTHW SFMLGEIALY SFIVLLLSGV YLTLFFDPSM SEVTYNGIYQ PLRGVQMSK AYETTLNISF EVRGGLFVRQ IHHWAALMFA ASIMVHMARI FFTGAFRRPR EANWVIGALL FILAMFEGFF G YSLPDDLL SGTGIRAALS GITMGLPLIG TWMHWALFGG DFPGNILIPR LYAMHILLIP AIILALIGIH LALVWYQKHT QF PGPGATE KNVVGVRILP VFALKGGSFF AFTTAILALM SGLLQINPIW VLGPYKPSQI SAGSQPDFYM MWTDGLLRII PAW EIYPFG HTIPQAVWVA VGMGLVFGLL IAYPFLEKKL TGDDAHHNLL QRPRDAPVRT AIGSAAISLY MLFTLMCMND IIAL KFHIS LNATTWIGRI GMVILPAVVY YIAYRWAIGL QRSDRAVLEH GIETGIIKRL PHGEYIEIHQ PLAGVDEHGH AIPLE YQGA PVPQRMNKLG SAGAPGTGSF LFADPADEQH ALAEAEHEAH HKSLLALKEY QDGEPSTNGH GH

UniProtKB: Cytochrome bc1 complex cytochrome b subunit

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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: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 18.192475 KDa
SequenceString:
MTRMGTATAT PAPRRLEGPQ VASGDVAVKP AGDLPRGWAE TVSGRLSGVT EPGELSVHYP FPNYQLATLD DALTYGSRQS KARFSVYIG DLGNDTNAGA REVFLKVPTP DEAVLIAVSP DQHVVEVVYG EALKGRGAES AADLGVAAAL AAFKEGNLLD G IISAVRVM SAAIARP

UniProtKB: DUF5130 domain-containing protein

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Macromolecule #11: Cytochrome c oxidase polypeptide 4

MacromoleculeName: Cytochrome c oxidase polypeptide 4 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: cytochrome-c oxidase
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 15.068367 KDa
SequenceString:
MHIEARLFEI LTGFFALATV VYAVLTAMYA NGGVEWAGTT AMVMTTGLSL IISTFFRFVA RRLDTRPEDY EDAEIADGAG ELGFYSPHS WWPIMIALAA ATTAVGVALW LPWLLAAGAV FVLSAVAGLV FEYHIGAEKH

UniProtKB: Cytochrome c oxidase polypeptide 4

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Macromolecule #12: Lipoprotein lpqE

MacromoleculeName: Lipoprotein lpqE / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 23.241809 KDa
SequenceString: MFRTRSRRST TRVTTLLGAA VLATALTGCG AGQISQTANQ SSAINGGSAN LGKLALRNIH LVGNSDPVKQ RAGQKAELVL VIANESADI SDKLTSITSP DEIGKVTLSG DSDIPATGRL FVGSAEGQEP PAEAKAPETA APEAGSTEIT TAVTPAPEAK P QASSDPAI ...String:
MFRTRSRRST TRVTTLLGAA VLATALTGCG AGQISQTANQ SSAINGGSAN LGKLALRNIH LVGNSDPVKQ RAGQKAELVL VIANESADI SDKLTSITSP DEIGKVTLSG DSDIPATGRL FVGSAEGQEP PAEAKAPETA APEAGSTEIT TAVTPAPEAK P QASSDPAI KHGKAQLTLT KDLADGLTYR FTFTFEKAGE VTVAVPIDAG PNAPRQHTID GGGHEGGEH

UniProtKB: Lipoprotein lpqE

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Macromolecule #13: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate

MacromoleculeName: (2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
type: ligand / ID: 13 / 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 #14: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 14 / Number of copies: 18 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #15: (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: 15 / Number of copies: 6 / 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 #16: HEME-A

MacromoleculeName: HEME-A / type: ligand / ID: 16 / Number of copies: 4 / Formula: HEA
Molecular weightTheoretical: 852.837 Da
Chemical component information

ChemComp-HEA:
HEME-A

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Macromolecule #17: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 17 / Number of copies: 8 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Macromolecule #18: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 18 / Number of copies: 2 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #19: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 19 / Number of copies: 2 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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Macromolecule #20: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 20 / Number of copies: 6 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #21: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 21 / 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 #22: (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: 22 / Number of copies: 6 / 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 #23: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 23 / Number of copies: 10 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #24: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 24 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #25: water

MacromoleculeName: water / type: ligand / ID: 25 / Number of copies: 74 / 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

Concentration13 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 194219
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9wcx:
Cryo-EM structure of the Mycobacterium abscessus cytochrome bcc:aa3 supercomplex

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