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 [ Pubmed: 38347078 DOI: doi:10.1038/s42003-024-05863-w ]
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Bacteriochlorophyll a (911 Da, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Allochromatium vinosum DSM 180)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (2s)-3-hydroxypropane-1,2-diyl dihexadecanoate (568 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Allochromatium vinosum DSM 180)
- Ubiquinone-8 (727 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple sulfur phototrophic bacterium allochromatium vinosum (Complex from Allochromatium vinosum DSM 180)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Water (18 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Palmitic acid (256 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Magnesium ion (24 Da, Ligand)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium vinosum DSM 180)
- Spirilloxanthin (596 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 ]
- Reaction center protein m chain (36 kDa, Protein from Allochromatium vinosum DSM 180)
- (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)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Calcium ion (40 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic lh1-rc complex from the purple sulfur phototrophic bacterium allochromatium vinosum (Complex from Allochromatium vinosum DSM 180)
- Reaction center protein l chain (31 kDa, Protein from Allochromatium vinosum DSM 180)
- Ubiquinone-8 (727 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- (2s)-3-hydroxypropane-1,2-diyl dihexadecanoate (568 Da, Ligand)
- Antenna complex alpha/beta subunit (7 kDa, Protein from Allochromatium vinosum DSM 180)
- Water (18 Da, Ligand)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium vinosum DSM 180)
- Antenna complex alpha/beta subunit (5 kDa, Protein from Allochromatium vinosum DSM 180)
- Menaquinone 8 (717 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Palmitic acid (256 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 [ Pubmed: 36792596 DOI: doi:10.1038/s41467-023-36460-w ]
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter capsulatus)
- (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)
- Myristic acid (228 Da, Ligand)
- Photosynthetic reaction center pufx protein (8 kDa, Protein from Rhodobacter capsulatus)
- Spheroidene (568 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodobacter capsulatus (Complex from Rhodobacter capsulatus)
- Water (18 Da, Ligand)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Rhodobacter capsulatus)
- Bacteriochlorophyll a (911 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter capsulatus)
- Light-harvesting protein b-870 beta chain (5 kDa, Protein from Rhodobacter capsulatus)
- Bacteriopheophytin a (889 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Light-harvesting protein b-870 alpha chain (6 kDa, Protein from Rhodobacter capsulatus)
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 7vrj
Q-score: 0.601
Tani K, Kobayashi K, Hosogi N, Ji XC, Nagashima S, Nagashima KVP, Izumida A, Inoue K, Tsukatani Y, Kanno R, Hall M, Yu LJ, Ishikawa I, Okura Y, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Wang-Otomo ZY
J Biol Chem (2022) 298 pp. 101967-101967 [ DOI: doi:10.1016/j.jbc.2022.101967 Pubmed: 35460693 ]
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Heme c (618 Da, Ligand)
- Photosynthetic reaction center m subunit (36 kDa, Protein from Allochromatium tepidum)
- Bacteriochlorophyll a (911 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Light-harvesting protein lh1 alpha3 (7 kDa, Protein from Allochromatium tepidum)
- Ubiquinone-8 (727 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (43 kDa, Protein from Allochromatium tepidum)
- Light-harvesting protein lh1 beta3 (5 kDa, Protein from Allochromatium tepidum)
- Light-harvesting protein lh1 alpha1 (7 kDa, Protein from Allochromatium tepidum)
- Water (18 Da, Ligand)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Light-harvesting protein lh1 alpha2 (5 kDa, Protein from Allochromatium tepidum)
- Palmitic acid (256 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium allochromatium tepidum (Complex from Allochromatium tepidum)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Allochromatium tepidum)
- Diacyl glycerol (625 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Magnesium ion (24 Da, Ligand)
- Light-harvesting protein lh1 beta1 (5 kDa, Protein from Allochromatium tepidum)
- Photosynthetic reaction center l subunit (31 kDa, Protein from Allochromatium tepidum)
- Spirilloxanthin (596 Da, Ligand)