Cryo-EM structure of the Rhodospirillum rubrum RC-LH1 complex
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 9k3q
Q-score: 0.534
To Be Published
- Reaction center_light harvesting complex 1 from rhodospirillum rubrum (Complex from Rhodospirillum rubrum)
- Reaction center protein m chain (29 kDa, Protein from Rhodospirillum rubrum)
- Light-harvesting protein b-870 beta chain (5 kDa, Protein from Rhodospirillum rubrum)
- Reaction center protein l chain (30 kDa, Protein from Rhodospirillum rubrum)
- Ubiquinone-10 (863 Da, Ligand)
- Trans-geranyl bacteriochlorophyll a (901 Da, Ligand)
- Photoreaction center protein h (27 kDa, Protein from Rhodospirillum rubrum)
- Bacteriopheophytin a (889 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Light-harvesting protein b-870 alpha chain (5 kDa, Protein from Rhodospirillum rubrum)
- Fe (iii) ion (55 Da, Ligand)
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 [ DOI: doi:10.1016/j.bbabio.2024.149050 Pubmed: 38806091 ]
- Lh1 beta polypeptide (5 kDa, Protein from Thermochromatium tepidum)
- Lh1 alpha polypeptide (6 kDa, Protein from Thermochromatium tepidum)
- Calcium ion (40 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Octadecane (254 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- 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 [ DOI: doi:10.1016/j.bbabio.2024.149050 Pubmed: 38806091 ]
- Lh1 alpha polypeptide (7 kDa, Protein from Thermochromatium tepidum)
- Calcium ion (40 Da, Ligand)
- Dodecane (170 Da, Ligand)
- Lh1 complex (Complex from Thermochromatium tepidum)
- Lh1 beta polypeptide (5 kDa, Protein from Thermochromatium tepidum)
- Bacteriochlorophyll a (911 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
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)
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 [ DOI: doi:10.1016/j.jbc.2023.105057 Pubmed: 37468106 ]
- (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)
- Bacteriochlorophyll a (911 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 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)
- Gamma-carotene (536 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Crt-less rc-lh core complex (Complex from Roseiflexus castenholzii)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Unknown ligand (691 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
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 [ DOI: doi:10.1016/j.jbc.2023.105057 Pubmed: 37468106 ]
- (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)
- Bacteriochlorophyll a (911 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- 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)
- Gamma-carotene (536 Da, Ligand)
- Reaction center small polypeptide (6 kDa, Protein from Roseiflexus castenholzii)
- Cytochrome subunit of photosynthetic reaction center (34 kDa, Protein from Roseiflexus castenholzii)
- Reaction center protein l chain (71 kDa, Protein from Roseiflexus castenholzii)
- [(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)
- Unknown ligand (Ligand)
- Tmx polypeptide (3 kDa, Protein from Roseiflexus castenholzii)
- Reaction center unknown polypeptide (740 Da, Protein from Roseiflexus castenholzii)
- Antenna complex alpha/beta subunit (6 kDa, Protein from Roseiflexus castenholzii)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Rc-lh core complex (Complex from Roseiflexus castenholzii)
- Reaction center small polypeptide (4 kDa, Protein from Roseiflexus castenholzii)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 10,000 lux
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8hju
Q-score: 0.603
Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X
eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]
- Fe (iii) ion (55 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Diacyl glycerol (625 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- The native rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- 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)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Cryo-EM structure of carotenoid-depleted RC-LH complex from Roseiflexus castenholzii at 10,000 lux
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8hjv
Q-score: 0.478
Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X
eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]
- Fe (iii) ion (55 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- The carotenoid-depleted rc-lh complex (Complex from Roseiflexus castenholzii DSM 13941)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- 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)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 100lux
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8j5o
Q-score: 0.606
Xin J, Shi Y, Zhang X, Yuan X, Xin Y, He H, Shen J, Blankenship RE, Xu X
eLife (2023) 12 [ Pubmed: 37737710 DOI: doi:10.7554/eLife.88951 ]
- Fe (iii) ion (55 Da, Ligand)
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Multiheme_cytc domain-containing protein (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- The native rc-lh complex at 100lux (Complex from Roseiflexus castenholzii DSM 13941)
- Subunit z (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Alpha subunit of light-harvesting 1 (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriochlorophyll a (911 Da, Ligand)
- Reaction center protein m chain (35 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit x (3 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Bacteriopheophytin a (889 Da, Ligand)
- Beta subunit of light-harvesting 1 (6 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- Subunit y (4 kDa, Protein from Roseiflexus castenholzii DSM 13941)
- 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)
- Beta,psi-caroten-4-one (550 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Reaction center protein l chain (34 kDa, Protein from Roseiflexus castenholzii DSM 13941)