The Cryo-EM structure of siphonaxanthin chlorophyll a/b type light-harvesting complex II
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7wlm
Q-score: 0.649
Seki S, Nakaniwa T, Castro-Hartmann P, Sader K, Kawamoto A, Tanaka H, Qian P, Kurisu G, Fujii R
Bba Adv (2022) 2 pp. 100064-100064 [ DOI: doi:10.1016/j.bbadva.2022.100064 Pubmed: 37082593 ]
- Siphonaxanthin chlorophyll a/b binding light-harvesting complex ii (24 kDa, Protein from Codium fragile)
- Siphonaxanthin chlorophyll a/b-type light-harvesting complex ii (119 kDa, Complex from Codium fragile)
- Siphonein (781 Da, Ligand)
- Siphonaxanthin (600 Da, Ligand)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Water (18 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
PucA-LH2 complex from Rps. palustris
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7zcu
Q-score: 0.612
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ DOI: doi:10.1073/pnas.2210109119 Pubmed: 36251992 ]
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris ATCC 17001)
- Bacteriochlorophyll a (911 Da, Ligand)
- 1,2-dihydro-psi,psi-caroten-1-ol (554 Da, Ligand)
- Light-harvesting protein b-800-850 beta chain (5 kDa, Protein from Rhodopseudomonas palustris ATCC 17001)
- Water (18 Da, Ligand)
- Light-harvesting protein b-800-850 alpha chain (6 kDa, Protein from Rhodopseudomonas palustris ATCC 17001)
- Puca-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
PucB-LH2 complex from Rps. palustris
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7zdi
Q-score: 0.607
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ DOI: doi:10.1073/pnas.2210109119 Pubmed: 36251992 ]
- Pucb-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
- Light-harvesting protein (5 kDa, Protein from Rhodopseudomonas palustris)
- Bacteriochlorophyll a (911 Da, Ligand)
- 1,2-dihydro-psi,psi-caroten-1-ol (554 Da, Ligand)
- Light-harvesting protein (6 kDa, Protein from Rhodopseudomonas palustris)
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris)
PucD-LH2 complex from Rps. palustris
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7ze3
Q-score: 0.614
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ DOI: doi:10.1073/pnas.2210109119 Pubmed: 36251992 ]
- Light-harvesting protein b-800-850 beta chain (5 kDa, Protein from Rhodopseudomonas palustris)
- (3'e)-3',4'-didehydro-1,2-dihydro-psi,psi-caroten-1-ol (552 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Light-harvesting protein b-800-850 alpha chain (6 kDa, Protein from Rhodopseudomonas palustris)
- Water (18 Da, Ligand)
- Pucd-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris)
PucE-LH2 complex from Rps. palustris
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7ze8
Q-score: 0.509
Qian P, Nguyen-Phan CT, Gardiner AT, Croll TI, Roszak AW, Southall J, Jackson PJ, Vasilev C, Castro-Hartmann P, Sader K, Hunter CN, Cogdell RJ
PNAS (2022) 119 pp. e2210109119-e2210109119 [ DOI: doi:10.1073/pnas.2210109119 Pubmed: 36251992 ]
- Light-harvesting protein (5 kDa, Protein from Rhodopseudomonas palustris)
- Bacteriochlorophyll a (911 Da, Ligand)
- Light-harvesting protein (6 kDa, Protein from Rhodopseudomonas palustris)
- 1,2-dihydro-psi,psi-caroten-1-ol (554 Da, Ligand)
- Puce-lh2 from rps. palustris (Complex from Rhodopseudomonas palustris ATCC 17001)
- Puca-lh2-gamma (10 kDa, Protein from Rhodopseudomonas palustris)
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 ]
- [(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-dlh model_1a (800 kDa, Complex 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~{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)
- Dodecyl-beta-d-maltoside (510 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)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Rc-m (41 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Water (18 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-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Spirilloxanthin (596 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)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Heme c (618 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 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 ]
- [(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)
- 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)
- Light-harvesting protein b:885 subunit beta (4 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)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Lhc 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)
- (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)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Water (18 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-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Spirilloxanthin (596 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-dlh (model_2a) (800 kDa, Complex from Gemmatimonas phototrophica)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Heme c (618 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 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 ]
- [(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)
- 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~{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)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Lhc 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)
- (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)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Water (18 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-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Spirilloxanthin (596 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)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Heme c (618 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh model_1b (800 kDa, Complex from Gemmatimonas phototrophica)
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 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 ]
- [(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)
- 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~{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)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Rc-u (13 kDa, Protein from Gemmatimonas phototrophica)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Photosynthetic reaction center l subunit (30 kDa, Protein from Gemmatimonas phototrophica)
- Rc-dlh model_2b (800 kDa, Complex from Gemmatimonas phototrophica)
- Rc-m (41 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)
- (2~{s},3~{s},4~{s},5~{s})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carboxylic acid (262 Da, Ligand)
- Prch domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lhh-alpha (6 kDa, Protein from Gemmatimonas phototrophica)
- Fe (iii) ion (55 Da, Ligand)
- Lhc domain-containing protein (7 kDa, Protein from Gemmatimonas phototrophica)
- Water (18 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-s (21 kDa, Protein from Gemmatimonas phototrophica)
- Spirilloxanthin (596 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)
- Light-harvesting protein b:885 subunit beta (5 kDa, Protein from Gemmatimonas phototrophica)
- Heme c (618 Da, Ligand)
- Rc-hc (20 kDa, Protein from Gemmatimonas phototrophica)
- Multiheme_cytc domain-containing protein (38 kDa, Protein from Gemmatimonas phototrophica)
- Bacteriopheophytin a (889 Da, Ligand)