Resolution: 2.67 Å
EM Method: Single-particle
Fitted PDBs: 7e1w
Q-score: 0.569
Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, Rao Z, Gong H
eLife (2021) 10 [ DOI: doi:10.7554/eLife.69418 Pubmed: 34819223 ]
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- (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 (853 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Heme c (618 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- 6-chloranyl-2-ethyl-n-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]imidazo[1,2-a]pyridine-3-carboxamide (557 Da, Ligand)
- Hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv in the presence of q203 (800 kDa, Complex from Mycolicibacterium smegmatis MC2 51)
- Water (18 Da, Ligand)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Heme-a (852 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 7e1x
Q-score: 0.513
Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, Rao Z, Gong H
eLife (2021) 10 [ DOI: doi:10.7554/eLife.69418 Pubmed: 34819223 ]
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- (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 (853 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Heme c (618 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Heme-a (852 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv in presence of tb47 (800 kDa, Complex from Mycolicibacterium smegmatis MC2 51)
- Mycobacterium tuberculosis complexiii (Complex)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- 5-methoxy-2-methyl-~{n}-[[4-[4-[4-(trifluoromethyloxy)phenyl]piperidin-1-yl]phenyl]methyl]pyrazolo[1,5-a]pyridine-3-carboxamide (538 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 7e1v
Q-score: 0.614
Zhou S, Wang W, Zhou X, Zhang Y, Lai Y, Tang Y, Xu J, Li D, Lin J, Yang X, Ran T, Chen H, Guddat LW, Wang Q, Gao Y, Rao Z, Gong H
eLife (2021) 10 [ DOI: doi:10.7554/eLife.69418 Pubmed: 34819223 ]
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- (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 (853 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Heme c (618 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Apo hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv (800 kDa, Complex from Mycolicibacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Heme-a (852 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Mycobacterium smegmatis complexiv (Complex)
- Mycobacterium tuberculosis complexiii (Complex from Mycobacterium tuberculosis H37Rv)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
Structure of Mycobacterium smegmatis bd complex in the apo-form.
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 7d5i
Q-score: 0.597
Wang W, Gao Y, Tang Y, Zhou X, Lai Y, Zhou S, Zhang Y, Yang X, Liu F, Guddat LW, Wang Q, Rao Z, Gong H
Nat Commun (2021) 12 pp. 4621-4621 [ DOI: doi:10.1038/s41467-021-24924-w Pubmed: 34330928 ]
- Integral membrane cytochrome d ubiquinol oxidase (subunit ii) cydb (39 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cis-heme d hydroxychlorin gamma-spirolactone (632 Da, Ligand)
- Cryo-em structure of mycobacterium smegmatis bd complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Cytochrome d ubiquinol oxidase subunit 1 (53 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme b/c (618 Da, Ligand)
Mycobacterium smegmatis Sdh1 in complex with UQ1
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 7d6v
Q-score: 0.636
Zhou X, Gao Y, Wang W, Yang X, Yang X, Liu F, Tang Y, Lam SM, Shui G, Yu L, Tian C, Guddat LW, Wang Q, Rao Z, Gong H
PNAS (2021) 118 [ Pubmed: 33876763 DOI: doi:10.1073/pnas.2022308118 ]
- Fe3-s4 cluster (295 Da, Ligand)
- Succinate dehydrogenase subunit a (70 kDa, Protein from Mycolicibacterium smegmatis)
- Fumarate reductase iron-sulfur subunit (28 kDa, Protein from Mycolicibacterium smegmatis)
- Ubiquinone-1 (250 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Mycobacterium smegmatis sdh1 in complex with uq1 (Complex from Mycolicibacterium smegmatis MC2 51)
- Succinate dehydrogenase (membrane anchor subunit) (32 kDa, Protein from Mycolicibacterium smegmatis)
- (1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (720 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Mycobacterium smegmatis Sdh1 complex in the apo form
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 7d6x
Q-score: 0.587
Zhou X, Gao Y, Wang W, Yang X, Yang X, Liu F, Tang Y, Lam SM, Shui G, Yu L, Tian C, Guddat LW, Wang Q, Rao Z, Gong H
PNAS (2021) 118 [ Pubmed: 33876763 DOI: doi:10.1073/pnas.2022308118 ]
- Fe3-s4 cluster (295 Da, Ligand)
- Succinate dehydrogenase subunit a (70 kDa, Protein from Mycolicibacterium smegmatis)
- Fumarate reductase iron-sulfur subunit (28 kDa, Protein from Mycolicibacterium smegmatis)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Succinate dehydrogenase (membrane anchor subunit) (32 kDa, Protein from Mycolicibacterium smegmatis)
- Mycobacterium smegmatis sdh1 complex in apo form (Complex from Mycolicibacterium smegmatis MC2 51)
- (1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate (720 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Mycobacterium smegmatis SugABC complex
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 7cad
Q-score: 0.505
Liu F, Liang J, Zhang B, Gao Y, Yang X, Hu T, Yang H, Xu W, Guddat LW, Rao Z
Sci Adv (2020) 6 [ DOI: doi:10.1126/sciadv.abb9833 Pubmed: 33127676 ]
- Mycobacterium smegmatis sugabc complex (Complex from Mycolicibacterium smegmatis MC2 155)
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Abc transporter, atp-binding protein sugc (43 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Abc transporter, permease protein sugb (29 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Mycobacterium smegmatis LpqY-SugABC complex in the resting state
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 7cae
Q-score: 0.491
Liu F, Liang J, Zhang B, Gao Y, Yang X, Hu T, Yang H, Xu W, Guddat LW, Rao Z
Sci Adv (2020) 6 [ DOI: doi:10.1126/sciadv.abb9833 Pubmed: 33127676 ]
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Abc transporter, atp-binding protein sugc (43 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Mycobacterium smegmatis lpqy-sugabc complex in the resting state. (Complex from Mycolicibacterium smegmatis MC2 155)
- Abc transporter, permease protein sugb (29 kDa, Protein from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Mycobacterium smegmatis LpqY-SugABC complex in the pre-translocation state
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7caf
Q-score: 0.498
Liu F, Liang J, Zhang B, Gao Y, Yang X, Hu T, Yang H, Xu W, Guddat LW, Rao Z
Sci Adv (2020) 6 [ DOI: doi:10.1126/sciadv.abb9833 Pubmed: 33127676 ]
- Abc transporter, permease protein sugb (29 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Abc transporter, atp-binding protein sugc (43 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Bacterial extracellular solute-binding protein (50 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Abc sugar transporter, permease component (32 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterium smegmatis lpqy-sugabc complex in the pre-translocation state (Complex from Mycolicibacterium smegmatis MC2 155)