CIII2/CIV respiratory supercomplex from Mycobacterium smegmatis with lansoprazole sulfide
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9ftz
Q-score: 0.608
Kovalova T, Krol S, Gamiz-Hernandez AP, Sjostrand D, Kaila VRI, Brzezinski P, Hogbom M
PNAS (2024) 121 pp. e2412780121-e2412780121 [ DOI: doi:10.1073/pnas.2412780121 Pubmed: 39531492 ]
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- (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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Lansoprazole sulfide (353 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Calcium ion (40 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Tridecane (184 Da, Ligand)
- Heme c (618 Da, 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)
- Water (18 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
CIII2/CIV respiratory chain supercomplex from Mycobacterium smegmatis
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9fu0
Q-score: 0.573
Kovalova T, Krol S, Gamiz-Hernandez AP, Sjostrand D, Kaila VRI, Brzezinski P, Hogbom M
PNAS (2024) 121 pp. e2412780121-e2412780121 [ DOI: doi:10.1073/pnas.2412780121 Pubmed: 39531492 ]
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- (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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Calcium ion (40 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Tridecane (184 Da, Ligand)
- Heme c (618 Da, 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)
- Water (18 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
Mycobacterial supercomplex malate:quinone oxidoreductase assembly
Di Trani JM, Yu J, Courbon GM, Lobez Rodriguez AP, Cheung CY, Liang Y, Coupland CE, Bueler SA, Cook GM, Brzezinski P, Rubinstein JL
PNAS (2025) 122 pp. e2423761122-e2423761122 [ DOI: doi:10.1073/pnas.2423761122 Pubmed: 39969994 ]
- (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 (16 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Palmitic acid (256 Da, Ligand)
- Probable malate:quinone oxidoreductase (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 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 bc1 complex cytochrome b subunit (59 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome aa3 subunit 2 (35 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Conserved transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Superoxide dismutase [cu-zn] (21 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome c oxidase subunit 1 (63 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Uncharacterized protein msmeg_4692/msmei_4575 (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase subunit ctaj (8 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome bc1 complex cytochrome c subunit (23 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Heme c (618 Da, Ligand)
- Cytochrome aa3 subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex rieske iron-sulfur subunit (42 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Respiratory complex mqo:ciii2civ2sod2 from mycobacterium smegmatis (Complex from Mycolicibacterium smegmatis MC2 155)
Di Trani JM, Yu J, Courbon GM, Lobez Rodriguez AP, Cheung CY, Liang Y, Coupland CE, Bueler SA, Cook GM, Brzezinski P, Rubinstein JL
PNAS (2025) 122 pp. e2423761122-e2423761122 [ DOI: doi:10.1073/pnas.2423761122 Pubmed: 39969994 ]
Di Trani JM, Yu J, Courbon GM, Lobez Rodriguez AP, Cheung CY, Liang Y, Coupland CE, Bueler SA, Cook GM, Brzezinski P, Rubinstein JL
PNAS (2025) 122 pp. e2423761122-e2423761122 [ DOI: doi:10.1073/pnas.2423761122 Pubmed: 39969994 ]
III2IV respiratory supercomplex from Saccharomyces cerevisiae
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 9etz
Q-score: 0.639
Lobez AP, Wu F, Di Trani JM, Rubinstein JL, Oliveberg M, Brzezinski P, Moe A
Nat Commun (2024) 15 pp. 8241-8241 [ Pubmed: 39300056 DOI: doi:10.1038/s41467-024-52475-3 ]
- Cytochrome c oxidase subunit 26, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase subunit 1 (58 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 2, mitochondrial (38 kDa, Protein from Saccharomyces cerevisiae)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase subunit 3 (30 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 12, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 4, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae)
- Iii2-iv respiratory supercomplex (Complex from Saccharomyces cerevisiae)
- Cytochrome b (43 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 7, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 2 (26 kDa, Protein from Saccharomyces cerevisiae)
- 5-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy-6-methyl-benzene-1,4-diol (592 Da, Ligand)
- Cytochrome b-c1 complex subunit 6, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 13, mitochondrial (13 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phoshocholine (734 Da, Ligand)
- Cytochrome c oxidase subunit 5a, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c1, heme protein, mitochondrial (27 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 1, mitochondrial (47 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 8, mitochondrial (10 kDa, Protein from Saccharomyces cerevisiae)
- Heme c (618 Da, Ligand)
- Cytochrome b-c1 complex subunit 7, mitochondrial (14 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome b-c1 complex subunit 10, mitochondrial (8 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 9, mitochondrial (6 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (20 kDa, Protein from Saccharomyces cerevisiae)
- Dinuclear copper ion (127 Da, Ligand)
- Cytochrome c oxidase subunit 6, mitochondrial (12 kDa, Protein from Saccharomyces cerevisiae)
- Cytochrome c oxidase subunit 8, mitochondrial (5 kDa, Protein from Saccharomyces cerevisiae)
III2IV respiratory supercomplex from Saccharomyces cerevisiae (consensus map)
Lobez AP, Wu F, Di Trani JM, Rubinstein JL, Oliveberg M, Brzezinski P, Moe A
Nat Commun (2024) 15 pp. 8241-8241 [ Pubmed: 39300056 DOI: doi:10.1038/s41467-024-52475-3 ]
Local refinement of CIII2 from Saccharomyces cerevisiae
Lobez AP, Wu F, Di Trani JM, Rubinstein JL, Oliveberg M, Brzezinski P, Moe A
Nat Commun (2024) 15 pp. 8241-8241 [ Pubmed: 39300056 DOI: doi:10.1038/s41467-024-52475-3 ]
Local refinement of CIV from Saccharomyces cerevisiae
Lobez AP, Wu F, Di Trani JM, Rubinstein JL, Oliveberg M, Brzezinski P, Moe A
Nat Commun (2024) 15 pp. 8241-8241 [ Pubmed: 39300056 DOI: doi:10.1038/s41467-024-52475-3 ]
Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8ovc
Q-score: 0.598
Riepl D, Gamiz-Hernandez AP, Kovalova T, Krol SM, Mader SL, Sjostrand D, Hogbom M, Brzezinski P, Kaila VRI
Nat Commun (2024) 15 pp. 5276-5276 [ Pubmed: 38902248 DOI: doi:10.1038/s41467-024-49628-9 ]
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- Fe2/s2 (inorganic) cluster (175 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-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (869 Da, Protein from Mycolicibacterium smegmatis)
- Calcium ion (40 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Heme-a (852 Da, Ligand)
- Heme c (618 Da, Ligand)
- Water (18 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (2 kDa, Protein from Mycolicibacterium smegmatis)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)