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)
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 RHODOBACTER SPHAEROIDES MONOMER
Resolution: 2.94 Å
EM Method: Single-particle
Fitted PDBs: 7f0l
Q-score: 0.597
Tani K, Nagashima KVP, Kanno R, Kawamura S, Kikuchi R, Hall M, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY
Nat Commun (2021) 12 pp. 6300-6300 [ DOI: doi:10.1038/s41467-021-26561-9 Pubmed: 34728609 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodobacter sphaeroides monomer (Complex from Rhodobacter sphaeroides f. sp. denitrificans)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Rhodobacter sphaeroides)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosynthetic reaction center l subunit (31 kDa, Protein from Rhodobacter sphaeroides)
- Antenna pigment protein beta chain (5 kDa, Protein from Rhodobacter sphaeroides)
- Spheroidene (568 Da, Ligand)
- Pufx (9 kDa, Protein from Rhodobacter sphaeroides)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter sphaeroides)
- Ubiquinone-10 (863 Da, Ligand)
- Protein-u (5 kDa, Protein from Rhodobacter sphaeroides)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Rhodobacter sphaeroides)
- (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)
- Reaction center protein h chain (28 kDa, Protein from Rhodobacter sphaeroides)
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOSPIRILLUM RUBRUM
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7eqd
Q-score: 0.577
Tani K, Kanno R, Ji XC, Hall M, Yu LJ, Kimura Y, Madigan MT, Mizoguchi A, Humbel BM, Wang-Otomo ZY
Biochemistry (2021) [ Pubmed: 34323477 DOI: doi:10.1021/acs.biochem.1c00360 ]
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodospirillum rubrum (Complex from Rhodospirillum rubrum)
- Trans-geranyl bacteriochlorophyll a (901 Da, Ligand)
- 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)
- Light-harvesting protein b-870 beta chain (6 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1))
- Photoreaction center protein h (27 kDa, Protein from Rhodospirillum rubrum)
- Trans-geranyl bacteriopheophytin a (879 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Light-harvesting protein b-870 alpha chain (7 kDa, Protein from Rhodospirillum rubrum)
- Ubiquinone-10 (863 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1))
- Cardiolipin (1 kDa, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Reaction center protein l chain (30 kDa, Protein from Rhodospirillum rubrum)
- (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)
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)