Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7qhm
Q-score: 0.567
Kao WC, Ortmann de Percin Northumberland C, Cheng TC, Ortiz J, Durand A, von Loeffelholz O, Schilling O, Biniossek ML, Klaholz BP, Hunte C
Nat Commun (2022) 13 pp. 545-545 [ DOI: doi:10.1038/s41467-022-28179-x Pubmed: 35087070 ]
- Heme c (618 Da, Ligand)
- Hypothetical membrane protein (12 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Heme-as (920 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Calcium ion (40 Da, Ligand)
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cardiolipin (1 kDa, Ligand)
- [(2~{r})-3-[[(1~{s},2~{r},3~{s},4~{s},5~{r},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-[[(2~{s},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,5-bis(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-3,4,5-tris(oxidanyl)-6-(undecanoyloxymethyl)oxan-2-yl]oxy-cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{r})-10-methyldodecanoate (1 kDa, Ligand)
- Thiamine biosynthesis protein x (17 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Diacyl glycerol (625 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Oxygen molecule (31 Da, Ligand)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Water (18 Da, Ligand)
- Cytochrome bcc-aa3 supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Copper (ii) ion (63 Da, Ligand)
- [(2~{r})-3-[[(1~{s},2~{r},3~{r},4~{s},5~{s},6~{r})-2-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hexadecanoyloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-[(2~{r},3~{s},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4,5-tris(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-2-undecanoyloxy-propyl] (10~{s})-10-methylhenicosanoate (1 kDa, Ligand)
- Azide ion (42 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)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Dinuclear copper ion (127 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome c oxidase subunit 2 (36 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Uncharacterized protein cgl2664/cg2949 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Lycopene (536 Da, Ligand)
- Stigmatellin a (514 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
III2-IV2 respiratory supercomplex from Corynebacterium glutamicum
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7q21
Q-score: 0.571
Moe A, Kovalova T, Krol S, Yanofsky DJ, Bott M, Sjostrand D, Rubinstein JL, Hogbom M, Brzezinski P
Structure (2022) 30 pp. 338- [ DOI: doi:10.1016/j.str.2021.11.008 Pubmed: 34910901 ]
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Cytochrome bc1 complex rieske iron-sulfur subunit (45 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Tridecane (184 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase subunit 1 (66 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Uncharacterized membrane protein cgl2017/cg2211 (16 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase subunit 2 (39 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Actinobacterial supercomplex, subunit c (ascc) (8 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Docosane (310 Da, Ligand)
- The respiratory supercomplex (Complex from Corynebacterium glutamicum ATCC 13032)
- Menaquinone-9 (785 Da, Ligand)
- Co-purified unknown transmembrane helices built as polyala (ascd) (8 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Heme-as (920 Da, Ligand)
- Hypothetical membrane protein (6 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Co-purified unknown peptide built as polyala (asce) (1 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Cytochrome bc1 complex cytochrome b subunit (59 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Uncharacterized protein cgl2664/cg2949 (20 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- (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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Co-purified unknown peptide built as polyala (asce) (1 kDa, Protein from Corynebacterium glutamicum ATCC 13032)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
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 ]
- Heme c (618 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)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 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)
- 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)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium 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)
- Water (18 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 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)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
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 ]
- Heme c (618 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)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium 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)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 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)
- 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)
- 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)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)
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 ]
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Mycobacterium tuberculosis complexiii (Complex from Mycobacterium tuberculosis H37Rv)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Prokaryotic respiratory supercomplex associate factor 1 prsaf1 (11 kDa, Protein from Mycolicibacterium 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)
- Cytochrome bc1 complex rieske iron-sulfur subunit (46 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome b subunit (61 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 1 (64 kDa, Protein from Mycolicibacterium smegmatis MC2 51)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 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)
- Cardiolipin (1 kDa, Ligand)
- Mycobacterium smegmatis complexiv (Complex)
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis MC2 51)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycobacterium tuberculosis H37Rv)