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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)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 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~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 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-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- Rc-dlh model_1a (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)
- (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)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- Rc-m (41 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)
- Menaquinone 8 (717 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 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)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Light-harvesting protein b:885 subunit beta (4 kDa, Protein from Gemmatimonas phototrophica)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 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~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein 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)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- (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)
- (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)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh (model_2a) (800 kDa, Complex from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 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)
- Menaquinone 8 (717 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 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)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 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_1b (800 kDa, Complex from Gemmatimonas phototrophica)
- [(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)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein 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)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- (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)
- (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)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 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)
- Bacteriopheophytin a (889 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 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)
- Rc-dlh model_2b (800 kDa, Complex from Gemmatimonas phototrophica)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 2-acetamido-2-deoxy-alpha-d-glucopyranose (221 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~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-octadecanoyloxy-propyl] octadecanoate (787 Da, Ligand)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein 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)
- Rc-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Heme c (618 Da, Ligand)
- (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)
- (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)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 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)
- Bacteriopheophytin a (889 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Water (18 Da, Ligand)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7oy8
Q-score: 0.551
Qian P, Croll TI, Swainsbury DJK, Castro-Hartmann P, Moriarty NW, Sader K, Hunter CN
Biochem J (2021) 478 pp. 3253-3263 [ DOI: doi:10.1042/BCJ20210511 Pubmed: 34402504 ]
- Rc-lh1 from rhodospirillum rubrum (297 MDa, Complex from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
- 2-azanyl-5-[(2~{e},6~{e},8~{e},10~{e},12~{e},14~{e},18~{e},22~{e},26~{e},30~{e},34~{e})-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,8,10,12,14,18,22,26,30,34,38-dodecaenyl]-3-methoxy-6-methyl-cyclohexa-2,5-diene-1,4-dione (844 Da, Ligand)
- Phosphate ion (94 Da, Ligand)
- Trans-geranyl bacteriochlorophyll a (901 Da, Ligand)
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
- (1r)-2-{[(s)-{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9z)-octadec-9-enoate (749 Da, Ligand)
- Antenna complex, alpha/beta subunit (5 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
- Light-harvesting protein b-870 beta chain (6 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
- Chloride ion (35 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- (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)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
- Ubiquinone-10 (863 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Photosynthetic reaction center, h-chain (27 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1))
- Water (18 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)