Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-translocation state
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8j5q
Q-score: 0.519
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B
Nat Struct Mol Biol (2024) [ Pubmed: 38548954 DOI: doi:10.1038/s41594-024-01256-z ]
- Iron/sulfur cluster (351 Da, Ligand)
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the pre-translocation state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Endogenous oligopeptide (783 Da, Protein from Mycolicibacterium smegmatis MC2 155)
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the resting state
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 8j5r
Q-score: 0.534
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B
Nat Struct Mol Biol (2024) [ Pubmed: 38548954 DOI: doi:10.1038/s41594-024-01256-z ]
- Iron/sulfur cluster (351 Da, Ligand)
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the resting state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the pre-catalytic intermediate state
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8j5s
Q-score: 0.566
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B
Nat Struct Mol Biol (2024) [ Pubmed: 38548954 DOI: doi:10.1038/s41594-024-01256-z ]
- Iron/sulfur cluster (351 Da, Ligand)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Endogenous oligopeptide (698 Da, Protein from Mycolicibacterium smegmatis MC2 155)
- Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the pre-catalytic intermediate state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Magnesium ion (24 Da, Ligand)
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Cryo-EM structure of Mycobacterium tuberculosis OppABCD in the catalytic intermediate state
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8j5t
Q-score: 0.572
Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B
Nat Struct Mol Biol (2024) [ Pubmed: 38548954 DOI: doi:10.1038/s41594-024-01256-z ]
- Iron/sulfur cluster (351 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Cryo-em structure of mycobacterium tuberculosis oppabcd in the catalytic intermediate state (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1283c (35 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Magnesium ion (24 Da, Ligand)
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
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 [ Pubmed: 34819223 DOI: doi:10.7554/eLife.69418 ]
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cardiolipin (1 kDa, Ligand)
- 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)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Heme c (618 Da, 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 (853 Da, Ligand)
- Water (18 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Copper (ii) ion (63 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)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
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 [ Pubmed: 34819223 DOI: doi:10.7554/eLife.69418 ]
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cardiolipin (1 kDa, 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)
- 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)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Heme c (618 Da, Ligand)
- Mycobacterium tuberculosis complexiii (Complex)
- (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)
- Heme-a (852 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Copper (ii) ion (63 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
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 [ Pubmed: 34819223 DOI: doi:10.7554/eLife.69418 ]
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Mycobacterium smegmatis complexiv (Complex)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Heme c (618 Da, 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 (853 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Apo hybrid respiratory supercomplex consisting of mycobacterium tuberculosis complexiii and mycobacterium smegmatis complexiv (800 kDa, Complex from Mycolicibacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Mycobacterium tuberculosis complexiii (Complex from Mycobacterium tuberculosis H37Rv)
- Copper (ii) ion (63 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)