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)
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)
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)
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 ]
- 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)
III2-IV1 respiratory supercomplex from S. pombe
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8q1b
Q-score: 0.46
Moe A, Dimogkioka AR, Rapaport D, Ojemyr LN, Brzezinski P
PNAS (2023) 120 pp. e2307697120-e2307697120 [ Pubmed: 37939086 DOI: doi:10.1073/pnas.2307697120 ]
- Cardiolipin (1 kDa, Ligand)
- Probable mitochondrial-processing peptidase subunit beta (50 kDa, Protein from Schizosaccharomyces pombe)
- Unknown polypeptide (2 kDa, Protein from Schizosaccharomyces pombe)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Cytochrome c oxidase subunit 1 (59 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b-c1 complex subunit 8 (10 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b (43 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 2 (28 kDa, Protein from Schizosaccharomyces pombe)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 12, mitochondrial (10 kDa, Protein from Schizosaccharomyces pombe)
- Respiratory supercomplex factor 2 homolog c1565.01 (27 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c1, heme protein, mitochondrial (34 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b-c1 complex subunit 10 (9 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 4, mitochondrial (17 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 13, mitochondrial (15 kDa, Protein from Schizosaccharomyces pombe)
- Iii2-iv1 respiratory supercomplex (Complex from Schizosaccharomyces pombe)
- Calcium ion (40 Da, Ligand)
- Cytochrome c oxidase subunit 7 (6 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b-c1 complex subunit 9 (7 kDa, Protein from Schizosaccharomyces pombe)
- Ubiquinone-10 (863 Da, Ligand)
- Cytochrome c oxidase polypeptide viii, mitochondrial (7 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b-c1 complex subunit rieske, mitochondrial (24 kDa, Protein from Schizosaccharomyces pombe)
- 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)
- Heme c (618 Da, Ligand)
- Cytochrome c oxidase subunit 9, mitochondrial (6 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase polypeptide 5, mitochondrial (24 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b-c1 complex subunit 6 (24 kDa, Protein from Schizosaccharomyces pombe)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase subunit 6, mitochondrial (15 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b-c1 complex subunit 7 (16 kDa, Protein from Schizosaccharomyces pombe)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Cytochrome c oxidase subunit 3 (30 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome b-c1 complex subunit 2, mitochondrial (45 kDa, Protein from Schizosaccharomyces pombe)
cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8smr
Q-score: 0.608
Di Trani JM, Gheorghita AA, Turner M, Brzezinski P, Adelroth P, Vahidi S, Howell PL, Rubinstein JL
PNAS (2023) 120 pp. e2307093120-e2307093120 [ Pubmed: 37751552 DOI: doi:10.1073/pnas.2307093120 ]
- Ubiquinone-10 (863 Da, Ligand)
- Cytochrome c1 (26 kDa, Protein from Pseudomonas aeruginosa)
- (2r)-2-(methoxymethyl)-4-{[(25r)-spirost-5-en-3beta-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-beta-d-glucopyranoside (855 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Pseudomonas aeruginosa)
- Copper (ii) ion (63 Da, Ligand)
- Cbb3-type cytochrome c oxidase subunit (34 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome bc1-cbb3 supercomplex (374 MDa, Complex from Pseudomonas aeruginosa)
- Cytochrome-c oxidase (52 kDa, Protein from Pseudomonas aeruginosa)
- Cbb3-type cytochrome c oxidase subunit ii (22 kDa, Protein from Pseudomonas aeruginosa)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b (46 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome c4 (18 kDa, Protein from Pseudomonas aeruginosa)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cytochrome c5 (13 kDa, Protein from Pseudomonas aeruginosa)
cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8snh
Q-score: 0.613
Di Trani JM, Gheorghita AA, Turner M, Brzezinski P, Adelroth P, Vahidi S, Howell PL, Rubinstein JL
PNAS (2023) 120 pp. e2307093120-e2307093120 [ Pubmed: 37751552 DOI: doi:10.1073/pnas.2307093120 ]
- Ubiquinone-10 (863 Da, Ligand)
- Cytochrome c1 (26 kDa, Protein from Pseudomonas aeruginosa)
- (2r)-2-(methoxymethyl)-4-{[(25r)-spirost-5-en-3beta-yl]oxy}butyl 4-o-alpha-d-glucopyranosyl-beta-d-glucopyranoside (855 Da, Ligand)
- Ubiquinol-cytochrome c reductase iron-sulfur subunit (20 kDa, Protein from Pseudomonas aeruginosa)
- Cbb3-type cytochrome c oxidase subunit (33 kDa, Protein from Pseudomonas aeruginosa)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome-c oxidase (52 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome bc1-cbb3 supercomplex (374 MDa, Complex from Pseudomonas aeruginosa)
- Cbb3-type cytochrome c oxidase subunit ii (22 kDa, Protein from Pseudomonas aeruginosa)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome b (46 kDa, Protein from Pseudomonas aeruginosa)
- Cytochrome c4 (18 kDa, Protein from Pseudomonas aeruginosa)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Heme c (618 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cytochrome c5 (13 kDa, Protein from Pseudomonas aeruginosa)
Cytochrome c oxidase from Schizosaccharomyces pombe
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 8c8q
Q-score: 0.525
Moe A, Adelroth P, Brzezinski P, Nasvik Ojemyr L
Commun Chem (2023) 6 pp. 32-32 [ DOI: doi:10.1038/s42004-023-00827-3 Pubmed: 36797353 ]
- Unknown polypeptide (2 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 1 (59 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 2 (28 kDa, Protein from Schizosaccharomyces pombe)
- Magnesium ion (24 Da, Ligand)
- Cytochrome c oxidase subunit 12, mitochondrial (10 kDa, Protein from Schizosaccharomyces pombe)
- Respiratory supercomplex factor 2 homolog c1565.01 (27 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 4, mitochondrial (17 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 13, mitochondrial (15 kDa, Protein from Schizosaccharomyces pombe)
- Calcium ion (40 Da, Ligand)
- Cytochrome c oxidase subunit 7 (6 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase polypeptide viii, mitochondrial (7 kDa, Protein from Schizosaccharomyces pombe)
- Heme-a (852 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Cytochrome c oxidase (246 kDa, Complex from Schizosaccharomyces pombe)
- Cytochrome c oxidase subunit 9, mitochondrial (6 kDa, Protein from Schizosaccharomyces pombe)
- Cytochrome c oxidase polypeptide 5, mitochondrial (24 kDa, Protein from Schizosaccharomyces pombe)
- Copper (ii) ion (63 Da, Ligand)
- Cytochrome c oxidase subunit 6, mitochondrial (15 kDa, Protein from Schizosaccharomyces pombe)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Dinuclear copper ion (127 Da, Ligand)
- Cytochrome c oxidase subunit 3 (30 kDa, Protein from Schizosaccharomyces pombe)
Mycobacterial respiratory complex I with both quinone positions modelled
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8e9g
Q-score: 0.537
Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL
PNAS (2023) 120 pp. e2214949120-e2214949120 [ DOI: doi:10.1073/pnas.2214949120 Pubmed: 36952383 ]
- Menaquinone-9 (785 Da, Ligand)
- Nadh-quinone oxidoreductase subunit f (47 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit d (48 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Two-component system response regulator (14 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit c (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Flavin mononucleotide (456 Da, Ligand)
- Nadh-quinone oxidoreductase subunit a (13 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase, m subunit (56 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit i (19 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit k (10 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit b (20 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit g (83 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- (2r)-3-{[(r)-hydroxy({(1s,2r,3r,4r,5s,6s)-3,4,5-trihydroxy-2-(alpha-d-mannopyranosyloxy)-6-[(6-o-undecanoyl-beta-d-mannopyranosyl)oxy]cyclohexyl}oxy)phosphoryl]oxy}-2-(octanoyloxy)propyl undecanoate (1 kDa, Ligand)
- Zinc ion (65 Da, Ligand)
- Nadh-quinone oxidoreductase, l subunit (65 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit n (54 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit e (25 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Mycobacterial respiratory complex i, consensus map (560 kDa, Complex from Mycolicibacterium smegmatis MC2 155)
- Nadh-quinone oxidoreductase subunit h (44 kDa, Protein from Mycolicibacterium smegmatis MC2 155)
- Iron/sulfur cluster (351 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Nadh-quinone oxidoreductase subunit j (26 kDa, Protein from Mycolicibacterium smegmatis MC2 155)