Cryo-EM structure of the LH1 complex from thermochromatium tepidum
Resolution: 3.11 Å
EM Method: Single-particle
Fitted PDBs: 8jc8
Q-score: 0.575
Yan YH, Wang GL, Yue XY, Ma F, Madigan MT, Wang-Otomo ZY, Zou MJ, Yu LJ
Biochim Biophys Acta Bioenerg (2024) 1865 pp. 149050-149050 [ Pubmed: 38806091 DOI: doi:10.1016/j.bbabio.2024.149050 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Lh1 alpha polypeptide (6 kDa, Protein from Thermochromatium tepidum)
- Octadecane (254 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Lh1 beta polypeptide (5 kDa, Protein from Thermochromatium tepidum)
- Lh1 complex (Complex from Thermochromatium tepidum)
Cryo-EM structure of the LH1 complex from thermochromatium tepidum
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 8jc9
Q-score: 0.549
Yan YH, Wang GL, Yue XY, Ma F, Madigan MT, Wang-Otomo ZY, Zou MJ, Yu LJ
Biochim Biophys Acta Bioenerg (2024) 1865 pp. 149050-149050 [ Pubmed: 38806091 DOI: doi:10.1016/j.bbabio.2024.149050 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Lh1 alpha polypeptide (7 kDa, Protein from Thermochromatium tepidum)
- Calcium ion (40 Da, Ligand)
- Dodecane (170 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Lh1 beta polypeptide (5 kDa, Protein from Thermochromatium tepidum)
- Lh1 complex (Complex from Thermochromatium tepidum)
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8wdu
Q-score: 0.676
Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY
Commun Biol (2024) 7 pp. 176-176 [ DOI: doi:10.1038/s42003-024-05863-w Pubmed: 38347078 ]
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Bacteriochlorophyll a (911 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Reaction center protein l chain (31 kDa, Protein from Allochromatium vinosum DSM 180)
- Spirilloxanthin (596 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple sulfur phototrophic bacterium allochromatium vinosum (Complex from Allochromatium vinosum DSM 180)
- (2s)-3-hydroxypropane-1,2-diyl dihexadecanoate (568 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Water (18 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Allochromatium vinosum DSM 180)
- Magnesium ion (24 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Allochromatium vinosum DSM 180)
- Ubiquinone-8 (727 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Calcium ion (40 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 8wdv
Q-score: 0.658
Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY
Commun Biol (2024) 7 pp. 176-176 [ DOI: doi:10.1038/s42003-024-05863-w Pubmed: 38347078 ]
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Bacteriochlorophyll a (911 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Reaction center protein l chain (31 kDa, Protein from Allochromatium vinosum DSM 180)
- Spirilloxanthin (596 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple sulfur phototrophic bacterium allochromatium vinosum (Complex from Allochromatium vinosum DSM 180)
- (2s)-3-hydroxypropane-1,2-diyl dihexadecanoate (568 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Water (18 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Allochromatium vinosum DSM 180)
- Magnesium ion (24 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Allochromatium vinosum DSM 180)
- Ubiquinone-8 (727 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Calcium ion (40 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Cryo-EM structure of the CRT-LESS RC-LH core complex from roseiflexus castenholzii
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8iun
Q-score: 0.613
Qi CH, Wang GL, Wang FF, Xin Y, Zou MJ, Madigan MT, Wang-Otomo ZY, Ma F, Yu LJ
J Biol Chem (2023) 299 pp. 105057-105057 [ Pubmed: 37468106 DOI: doi:10.1016/j.jbc.2023.105057 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Manganese (ii) ion (54 Da, Ligand)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Heme c (618 Da, Ligand)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
- Unknown ligand (691 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Gamma-carotene (536 Da, Ligand)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Calcium ion (40 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- 2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Crt-less rc-lh core complex (Complex from Roseiflexus castenholzii)
Cryo-EM structure of the RC-LH core complex from roseiflexus castenholzii
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 8iug
Q-score: 0.622
Qi CH, Wang GL, Wang FF, Xin Y, Zou MJ, Madigan MT, Wang-Otomo ZY, Ma F, Yu LJ
J Biol Chem (2023) 299 pp. 105057-105057 [ Pubmed: 37468106 DOI: doi:10.1016/j.jbc.2023.105057 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Unknown ligand (Ligand)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Manganese (ii) ion (54 Da, Ligand)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Heme c (618 Da, Ligand)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- Bacteriopheophytin a (889 Da, Ligand)
- [(2~{r},3~{s},4~{s},5~{r},6~{r})-6-[(6~{e},8~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{e},24~{e})-2,6,10,14,19,23-hexamethyl-25-(2,6,6-trimethylcyclohexen-1-yl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl pentadecanoate (941 Da, Ligand)
- Tmx polypeptide (3 kDa, Protein from Roseiflexus castenholzii)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Rc-lh core complex (Complex from Roseiflexus castenholzii)
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Gamma-carotene (536 Da, Ligand)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Calcium ion (40 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- 2-methyl-3-[(2e,6e,10e,14e,18e,22e,26e,30e,34e,38e)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione (921 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7yml
Q-score: 0.613
Tani K, Kanno R, Ji XC, Satoh I, Kobayashi Y, Hall M, Yu LJ, Kimura Y, Mizoguchi A, Humbel BM, Madigan MT, Wang-Otomo ZY
Nat Commun (2023) 14 pp. 846-846 [ DOI: doi:10.1038/s41467-023-36460-w Pubmed: 36792596 ]
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter capsulatus)
- Bacteriochlorophyll a (911 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Myristic acid (228 Da, Ligand)
- Water (18 Da, Ligand)
- Light-harvesting protein b-870 beta chain (5 kDa, Protein from Rhodobacter capsulatus)
- Fe (iii) ion (55 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter capsulatus)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Light-harvesting protein b-870 alpha chain (6 kDa, Protein from Rhodobacter capsulatus)
- Spheroidene (568 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodobacter capsulatus (Complex from Rhodobacter capsulatus)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Photosynthetic reaction center pufx protein (8 kDa, Protein from Rhodobacter capsulatus)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Rhodobacter capsulatus)
Structure of photosynthetic LH1-RC super-complex of Rhodopila globiformis
Resolution: 2.24 Å
EM Method: Single-particle
Fitted PDBs: 7xxf
Q-score: 0.676
Tani K, Kanno R, Kurosawa K, Takaichi S, Nagashima KVP, Hall M, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY
Commun Biol (2022) 5 pp. 1197-1197 [ DOI: doi:10.1038/s42003-022-04174-2 Pubmed: 36344631 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Rhodopila globiformis)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodopila globiformis (400 kDa, Complex from Rhodopila globiformis)
- Heme c (618 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (37 kDa, Protein from Rhodopila globiformis)
- Reaction center protein l chain (30 kDa, Protein from Rhodopila globiformis)
- Bacteriopheophytin a (889 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Water (18 Da, Ligand)
- Menaquinone-9 (785 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Light-harvesting protein (7 kDa, Protein from Rhodopila globiformis)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Rhodopila globiformis)
- Light-harvesting protein lh1 gamma-like (2 kDa, Protein from Rhodopila globiformis)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Light-harvesting protein (7 kDa, Protein from Rhodopila globiformis)
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (6~{e},8~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{e},24~{e},26~{e},28~{e})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26,28-dodecaen-5-one (612 Da, Ligand)
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF THIORHODOVIBRIO STRAIN 970
Resolution: 2.82 Å
EM Method: Single-particle
Fitted PDBs: 7c9r
Q-score: 0.632
Tani K, Kanno R, Makino Y, Hall M, Takenouchi M, Imanishi M, Yu LJ, Overmann J, Madigan MT, Kimura Y, Mizoguchi A, Humbel BM, Wang-Otomo ZY
Nat Commun (2020) 11 pp. 4955-4955 [ Pubmed: 33009385 DOI: doi:10.1038/s41467-020-18748-3 ]
- Photosynthetic reaction center, subunit h, bacterial (28 kDa, Protein from Thiorhodovibrio sp. 970)
- Bacteriochlorophyll a (911 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Thiorhodovibrio sp. 970)
- Lhc domain-containing protein (8 kDa, Protein from Thiorhodovibrio sp. 970)
- Octadecane (254 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Thiorhodovibrio sp. 970)
- (6~{e},8~{e},10~{e},12~{e},14~{e},16~{e},18~{e},20~{e},22~{e},24~{e},26~{e})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26-undecaene (600 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Light-harvesting-reaction center complex from the purple phototrophic bacterium thiorhodovibrio strain 970 (400 kDa, Complex from Thiorhodovibrio sp. 970)
- Fe (iii) ion (55 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Thiorhodovibrio sp. 970)
- Photosynthetic reaction center cytochrome c subunit (42 kDa, Protein from Thiorhodovibrio sp. 970)
- Antenna complex alpha/beta subunit (9 kDa, Protein from Thiorhodovibrio sp. 970)
- Cardiolipin (1 kDa, Ligand)
- Magnesium ion (24 Da, Ligand)
- Alpha subunit 1 of light-harvesting 1 complex (8 kDa, Protein from Thiorhodovibrio sp. 970)
- Alpha subunit 2 of light-harvesting 1 complex (9 kDa, Protein from Thiorhodovibrio sp. 970)
- Ubiquinone-8 (727 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Diacyl glycerol (625 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- L subunit of the reaction center (30 kDa, Protein from Thiorhodovibrio sp. 970)