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) [ DOI: doi:10.1038/s41594-024-01256-z Pubmed: 38548954 ]
- Iron/sulfur cluster (351 Da, Ligand)
- 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))
- 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))
- Magnesium ion (24 Da, Ligand)
- Putative peptide transport permease protein rv1282c (31 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Uncharacterized abc transporter atp-binding protein rv1281c (65 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
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) [ DOI: doi:10.1038/s41594-024-01256-z Pubmed: 38548954 ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Uncharacterized protein rv1280c (64 kDa, Protein from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
- Magnesium ion (24 Da, Ligand)
- Putative peptide transport permease protein rv1283c (35 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))
- 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 (Complex from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Cryo-EM structure of the 48-nm repeat doublet microtubule from mouse sperm
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8iyj
Q-score: 0.35
Zhou L, Liu H, Liu S, Yang X, Dong Y, Pan Y, Xiao Z, Zheng B, Sun Y, Huang P, Zhang X, Hu J, Sun R, Feng S, Zhu Y, Liu M, Gui M, Wu J
Cell (2023) 186 pp. 2897-2910.e19 [ Pubmed: 37295417 DOI: doi:10.1016/j.cell.2023.05.009 ]
- Sperm-associated antigen 8 (50 kDa, Protein from Mus musculus)
- Tektin-4 (52 kDa, Protein from Mus musculus)
- Outer dense fiber protein 3 (27 kDa, Protein from Mus musculus)
- Tubulin alpha-3 chain (50 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 68 (19 kDa, Protein from Mus musculus)
- Protein fam166c (23 kDa, Protein from Mus musculus)
- Tektin bundle-interacting protein 1 (23 kDa, Protein from Mus musculus)
- Ef-hand domain-containing family member c2 (87 kDa, Protein from Mus musculus)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tektin-3 (56 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 107 (23 kDa, Protein from Mus musculus)
- Ef-hand calcium-binding domain-containing protein 6 (176 kDa, Protein from Mus musculus)
- Protein phosphatase 1 regulatory subunit 32 (47 kDa, Protein from Mus musculus)
- Tektin-1 (48 kDa, Protein from Mus musculus)
- Piercer of microtubule wall 2 protein (13 kDa, Protein from Mus musculus)
- Meiosis-specific nuclear structural protein 1 (60 kDa, Protein from Mus musculus)
- Family with sequence similarity 183, member b (16 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 53 (62 kDa, Protein from Mus musculus)
- Testis expressed 49 (15 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 95 (26 kDa, Protein from Mus musculus)
- Dual specificity phosphatase 21 (21 kDa, Protein from Mus musculus)
- Spermatid-specific manchette-related protein 1 (29 kDa, Protein from Mus musculus)
- Cilia and flagella-associated protein 77 (32 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- Tubulin beta-4b chain (49 kDa, Protein from Mus musculus)
- Testis, prostate and placenta-expressed protein (24 kDa, Protein from Mus musculus)
- Rib43a-like with coiled-coils protein 2 (45 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 20 (22 kDa, Protein from Mus musculus)
- Mouse sperm dmt (Complex from Mus musculus)
- Rib43a-like with coiled-coils protein 1 (45 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 52 (68 kDa, Protein from Mus musculus)
- Coiled-coil domain-containing protein 105 (57 kDa, Protein from Mus musculus)
- Piercer of microtubule wall 1 protein (18 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 141 (12 kDa, Protein from Mus musculus)
- Protein fam166a (36 kDa, Protein from Mus musculus)
- Nucleoside diphosphate kinase 7 (44 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 276 (18 kDa, Protein from Mus musculus)
- Testis-specific serine/threonine-protein kinase 6 (30 kDa, Protein from Mus musculus)
- Enkurin (29 kDa, Protein from Mus musculus)
- Testis-expressed sequence 37 protein (21 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 45 (65 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 210 (65 kDa, Protein from Mus musculus)
- Testis-expressed protein 43 (16 kDa, Protein from Mus musculus)
- Protein flattop (20 kDa, Protein from Mus musculus)
- Ef-hand domain-containing family member b (95 kDa, Protein from Mus musculus)
- Tektin-2 (50 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 161 (34 kDa, Protein from Mus musculus)
- Uncharacterized protein c10orf82 homolog (25 kDa, Protein from Mus musculus)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Ef-hand domain-containing protein 1 (75 kDa, Protein from Mus musculus)
- Tektin-5 (62 kDa, Protein from Mus musculus)
- Cilia- and flagella-associated protein 90 (20 kDa, Protein from Mus musculus)
- Parkin coregulated gene protein homolog (27 kDa, Protein from Mus musculus)
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)
Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6adq
Q-score: 0.458
Gong H, Li J, Xu A, Tang Y, Ji W, Gao R, Wang S, Yu L, Tian C, Li J, Yen HY, Man Lam S, Shui G, Yang X, Sun Y, Li X, Jia M, Yang C, Jiang B, Lou Z, Robinson CV, Wong LL, Guddat LW, Sun F, Wang Q, Rao Z
Science (2018) 362 [ DOI: doi:10.1126/science.aat8923 Pubmed: 30361386 ]
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Superoxide dismutase in complex with bcc-aa3 type ciii-civ supercomplex from mycobacterium smegmatis (800 kDa, Complex from Mycobacterium smegmatis MC2 51)
- Cardiolipin (1 kDa, Ligand)
- Palmitic acid (256 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Ubiquinol-cytochrome c reductase cytochrome b subunit (60 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Fe2/s2 (inorganic) cluster (175 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)
- Copper (ii) ion (63 Da, Ligand)
- (2r)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (e)-octadec-9-enoate (717 Da, Ligand)
- Rieske iron-sulfur protein qcra (46 kDa, Protein from Mycobacterium smegmatis MC2 51)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 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)
- Lpqe protein (19 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Heme c (618 Da, Ligand)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (30 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Heme-a (852 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)