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 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- [(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)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Tridecane (184 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Lansoprazole sulfide (353 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein 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 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- [(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)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Tridecane (184 Da, Ligand)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
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 [ DOI: doi:10.1038/s41467-024-49628-9 Pubmed: 38902248 ]
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Heme c (618 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Co-purified unknown peptide (869 Da, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Heme-a (852 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- Copper (ii) ion (63 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Water (18 Da, Ligand)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Menaquinone-9 (785 Da, Ligand)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
- 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)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Co-purified unknown peptide (2 kDa, Protein from Mycolicibacterium smegmatis)
Respiratory supercomplex (III2-IV2) from Mycobacterium smegmatis
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8ovd
Q-score: 0.699
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 ]
- Cytochrome bc1 complex cytochrome c subunit (44 kDa, Protein from Mycolicibacterium smegmatis)
- Palmitic acid (256 Da, Ligand)
- Heme c (618 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- 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)
- Menaquinone-9 (785 Da, Ligand)
- Tridecane (184 Da, Ligand)
- Lpqe protein (19 kDa, Protein from Mycolicibacterium smegmatis)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- (2s)-1-(hexadecanoyloxy)propan-2-yl (10s)-10-methyloctadecanoate (594 Da, Ligand)
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycolicibacterium smegmatis)
- (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate (564 Da, Ligand)
- Water (18 Da, Ligand)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome-c oxidase (38 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome bc1 complex cytochrome c subunit (29 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycolicibacterium smegmatis)
- Superoxide dismutase [cu-zn] (23 kDa, Protein from Mycolicibacterium smegmatis)
- 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)
- The respiratory supercomplex (Complex from Mycolicibacterium smegmatis)
- Heme-a (852 Da, Ligand)
- Transmembrane protein (11 kDa, Protein from Mycolicibacterium smegmatis)
- Probable cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycolicibacterium smegmatis)
- Magnesium ion (24 Da, Ligand)
- Acyl-phosphatidyl-myo-inositol dimannoside (acpim2) (1 kDa, Ligand)
- Cytochrome bc1 complex cytochrome b subunit (61 kDa, Protein from Mycolicibacterium smegmatis)
- Cytochrome c oxidase subunit (8 kDa, Protein from Mycolicibacterium smegmatis)
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)
Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6hwh
Q-score: 0.5
Wiseman B, Nitharwal RG, Fedotovskaya O, Schafer J, Guo H, Kuang Q, Benlekbir S, Sjostrand D, Adelroth P, Rubinstein JL, Brzezinski P, Hogbom M
Nat Struct Mol Biol (2018) 25 pp. 1128-1136 [ DOI: doi:10.1038/s41594-018-0160-3 Pubmed: 30518849 ]
- Menaquinone-9 (785 Da, Ligand)
- Msmeg_4693 (8 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Cytochrome c oxidase subunit 3 (22 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Co-purified unknown peptide built as polyala (1 kDa, Protein from Mycobacterium smegmatis MC2 155)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (44 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Co-purified unknown transmembrane helices built as polyala (6 kDa, Protein from Mycobacterium smegmatis MC2 155)
- Cytochrome bc1 complex cytochrome c subunit (27 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Ubiquinol-cytochrome c reductase qcrb (61 kDa, Protein from Mycobacterium smegmatis MC2 155)
- Cytochrome c oxidase polypeptide 4 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Uncharacterized protein msmeg_4692/msmei_4575 (15 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Respiratory supercomplex from mycobacterium smegmatis (770 kDa, Complex from Mycobacterium smegmatis str. MC2 155)
- Cytochrome c oxidase subunit 1 (64 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Heme-as (920 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Co-purified unknown peptide built as polyala (2 kDa, Protein from Mycobacterium smegmatis MC2 155)
- Cytochrome c oxidase subunit 2 (38 kDa, Protein from Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
- Heme c (618 Da, Ligand)
- Co-purified unknown transmembrane helices built as polyala (5 kDa, Protein from Mycobacterium smegmatis MC2 155)
- Copper (ii) ion (63 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)