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Qian P, Gardiner AT, Šímová I, Naydenova K, Croll TI, Jackson PJ, Nupur N, Kloz M, Čubáková P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hájek J, Agirre J, Siebert CA, Bína D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polívka T, Hunter CN, Koblížek M
Sci Adv (2022) 8 [ DOI: 10.1126/sciadv.abk3139 Pubmed: 35171663 ]
Image sets:
Cryo-EM structure (model_1a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.4 A
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 7o0u
Q-score: 0.629
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- Water (18 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- Heme c (618 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh model_1a (800 kDa, Complex from Gemmatimonas phototrophica)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure (model_2a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.5 A
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7o0v
Q-score: 0.62
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- Water (18 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Light-harvesting protein b:885 subunit beta (4 kDa, Protein from Gemmatimonas phototrophica)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- Heme c (618 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Rc-dlh (model_2a) (800 kDa, Complex from Gemmatimonas phototrophica)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure of the RC-dLH complex (model_1b) from Gemmatimonas phototrophica at 2.47 A
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 7o0w
Q-score: 0.624
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- Water (18 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh model_1b (800 kDa, Complex from Gemmatimonas phototrophica)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- Heme c (618 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure (model_2b) of the RC-dLH complex from Gemmatimonas phototrophica at 2.44 A
Resolution: 2.44 Å
EM Method: Single-particle
Fitted PDBs: 7o0x
Q-score: 0.629
Qian P, Gardiner AT, Simova I, Naydenova K, Croll TI, Jackson PJ, Kloz M, Cubakova P, Kuzma M, Zeng Y, Castro-Hartmann P, van Knippenberg B, Goldie KN, Kaftan D, Hrouzek P, Hajek J, Agirre J, Siebert CA, Bina D, Sader K, Stahlberg H, Sobotka R, Russo CJ, Polivka T, Hunter CN, Koblizek M
Sci Adv (2022) 8 pp. eabk3139-eabk3139 [ Pubmed: 35171663 DOI: doi:10.1126/sciadv.abk3139 ]
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 Da, Ligand)
- Water (18 Da, Ligand)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh model_2b (800 kDa, Complex from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- (19r,22s)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22lambda~5~-phosphapentacosan-19-yl (9z)-hexadec-9-enoate (689 Da, Ligand)
- Heme c (618 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- [(2~{s})-3-[(2~{r},3~{r},4~{r},5~{s},6~{r})-6-(hydroxymethyl)-5-[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxy-2-(12-methyltridecanoyloxy)propyl] 12-methyltridecanoate (837 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- (2~{e},4~{e},6~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{z},24~{e},26~{e},28~{e})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid (610 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- (2r,5r,11r,14r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate (1 kDa, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Reaction centre light harvesting complex 1 from Blc. virids
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 6et5
Q-score: 0.469
Qian P, Siebert CA, Wang P, Canniffe DP, Hunter CN
Nature (2018) 556 pp. 203-208 [ Pubmed: 29618818 DOI: doi:10.1038/s41586-018-0014-5 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Bacteriochlorophyll b (909 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Rhodopseudomonas viridis)
- All-trans-1,2-dihydroneurosporene (540 Da, Ligand)
- 15-cis-1,2-dihydroneurosporene (540 Da, Ligand)
- Light-harvesting protein b-1015 gamma chain (2 kDa, Protein from Rhodopseudomonas viridis)
- Menaquinone-9 (785 Da, Ligand)
- Reaction center protein l chain (30 kDa, Protein from Rhodopseudomonas viridis)
- Bacteriopheophytin b (887 Da, Ligand)
- Light-harvesting protein b-1015 beta chain (6 kDa, Protein from Rhodopseudomonas viridis)
- Fe (iii) ion (55 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Reaction centre-light harvesting complex 1 (rc-lh1) (414 kDa, Complex from Blastochloris viridis)
- Light-harvesting protein b-1015 alpha chain (6 kDa, Protein from Rhodopseudomonas viridis)
- Sulfate ion (96 Da, Ligand)
- Reaction center protein m chain (35 kDa, Protein from Rhodopseudomonas viridis)
- Ubiquinone-9 (795 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (37 kDa, Protein from Rhodopseudomonas viridis)