Photosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila
Tani K, Nagashima KVP, Kojima R, Kondo M, Kanno R, Satoh I, Kawakami M, Hiwatashi N, Nakata K, Nagashima S, Inoue K, Isawa Y, Morishita R, Takaichi S, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Nagasawa Y, Dewa T, Wang-Otomo ZY
Nat Commun (2025) 16 pp. 1410-1410 [ DOI: doi:10.1038/s41467-024-55811-9 Pubmed: 39915441 ]
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
- Antenna complex, alpha/beta subunit (6 kDa, Protein from Halorhodospira halophila)
- (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 (8 kDa, Protein from Halorhodospira halophila)
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
- Spirilloxanthin (596 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosynthetic lh2-lh1 complex from the purple phototrophic bacterium halorhodospira halophila (Complex from Halorhodospira halophila)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lh2-lh1 complex of halorhodospira halophila (Complex from Halorhodospira halophila)
- Antenna complex, alpha/beta subunit (7 kDa, Protein from Halorhodospira halophila)
Structure of the Acidobacteria homodimeric reaction center bound with cytochrome c (the larger form)
Resolution: 2.61 Å
EM Method: Single-particle
Fitted PDBs: 7vzg
Q-score: 0.578
Dong S, Huang G, Wang C, Wang J, Sui SF, Qin X
Nat Commun (2022) 13 pp. 7745-7745 [ DOI: doi:10.1038/s41467-022-35460-6 Pubmed: 36517472 ]
- Pscd' (8 kDa, Protein from Chloracidobacterium thermophilum)
- [(2~{s})-2-[[(1~{r})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium (671 Da, Ligand)
- Heme c (618 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Psce (3 kDa, Protein from Chloracidobacterium thermophilum)
- Undefined polypeptide (1 kDa, Protein from Chloracidobacterium thermophilum)
- Cytochrome c domain-containing protein (15 kDa, Protein from Chloracidobacterium thermophilum)
- Pscg (4 kDa, Protein from Chloracidobacterium thermophilum)
- Unknown ligand (663 Da, Ligand)
- Water (18 Da, Ligand)
- Cabrc complex, the larger form (Complex from Chloracidobacterium thermophilum)
- Photosystem p840 reaction center iron-sulfur protein (8 kDa, Protein from Chloracidobacterium thermophilum)
- Chlorophyll a (893 Da, Ligand)
- [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~n~23~,n~24~,n~25~,n~26~]zinc (948 Da, Ligand)
- Pscf (3 kDa, Protein from Chloracidobacterium thermophilum)
- [(2s)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (649 Da, Ligand)
- [(2~{r})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (663 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Cytochrome c, mono-and diheme variants (22 kDa, Protein from Chloracidobacterium thermophilum)
- Psca (98 kDa, Protein from Chloracidobacterium thermophilum)
- Bacteriochlorophyll a (911 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)
Resolution: 2.22 Å
EM Method: Single-particle
Fitted PDBs: 7vzr
Q-score: 0.705
Dong S, Huang G, Wang C, Wang J, Sui SF, Qin X
Nat Commun (2022) 13 pp. 7745- [ DOI: doi:10.1038/s41467-022-35460-6 ]
- Cytochrome c domain-containing protein (15 kDa, Protein from Chloracidobacterium thermophilum B)
- Unknown ligand (671 Da, Ligand)
- [(2~{s})-2-[[(1~{r})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium (671 Da, Ligand)
- Heme c (618 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Photosynthetic reaction center subunit m (99 kDa, Protein from Chloracidobacterium thermophilum B)
- Pscg (5 kDa, Protein from Chloracidobacterium thermophilum B)
- Undefined polypeptide (1 kDa, Protein from Chloracidobacterium thermophilum)
- Psce (3 kDa, Protein from Chloracidobacterium thermophilum B)
- Water (18 Da, Ligand)
- Cabrc complex (Complex from Chloracidobacterium thermophilum)
- Chlorophyll a (893 Da, Ligand)
- Cytochrome c, mono-and diheme variants (24 kDa, Protein from Chloracidobacterium thermophilum B)
- [methyl 9-acetyl-14-ethyl-20-hydroxy-4,8,13,18-tetramethyl-3-{3-oxo-3-[(3,7,11,15-tetramethylhexadec-2-en-1-yl)oxy]propyl}-3,4,20,21-tetradehydrophorbine-21-carboxylatato(2-)-kappa~4~n~23~,n~24~,n~25~,n~26~]zinc (948 Da, Ligand)
- [(2s)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (649 Da, Ligand)
- [(2~{r})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (663 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Pscf (3 kDa, Protein from Chloracidobacterium thermophilum B)
- Bacteriochlorophyll a (911 Da, Ligand)
Photosynthetic assembly of Chlorobaculum tepidum (RC-FMO1)
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 7uea
Q-score: 0.406
Puskar R, Du Truong C, Swain K, Chowdhury S, Chan KY, Li S, Cheng KW, Wang TY, Poh YP, Mazor Y, Liu H, Chou TF, Nannenga BL, Chiu PL
Nat Commun (2022) 13 pp. 5824-5824 [ Pubmed: 36192412 DOI: doi:10.1038/s41467-022-33505-4 ]
- Cytochrome c (22 kDa, Protein from Chlorobaculum tepidum TLS)
- Photosynthetic assembly (rc-fmo1) (370 kDa, Complex from Chlorobaculum tepidum TLS)
- Photosystem p840 reaction center, large subunit (81 kDa, Protein from Chlorobaculum tepidum TLS)
- P840 reaction center 17 kda protein (16 kDa, Protein from Chlorobaculum tepidum TLS)
- Chlorophyll a ester (891 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriochlorophyll a protein (40 kDa, Protein from Chlorobaculum tepidum TLS)
- 2-[(1e,3e,5e,7e,9e,11e,13e,15e,17e,19e)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene (532 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- [(2r,3s,4s,5r,6r)-6-[(10e,12e,14e)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate (895 Da, Ligand)
- Bacteriochlorophyll a isomer (911 Da, Ligand)
- Photosystem p840 reaction center iron-sulfur protein (23 kDa, Protein from Chlorobaculum tepidum TLS)
Photosynthetic assembly of Chlorobaculum tepidum (RC-FMO2)
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 7ueb
Q-score: 0.497
Puskar R, Du Truong C, Swain K, Chowdhury S, Chan KY, Li S, Cheng KW, Wang TY, Poh YP, Mazor Y, Liu H, Chou TF, Nannenga BL, Chiu PL
Nat Commun (2022) 13 pp. 5824-5824 [ Pubmed: 36192412 DOI: doi:10.1038/s41467-022-33505-4 ]
- Pscf (6 kDa, Protein from Chlorobaculum tepidum TLS)
- Cytochrome c (22 kDa, Protein from Chlorobaculum tepidum TLS)
- Photosystem p840 reaction center, large subunit (81 kDa, Protein from Chlorobaculum tepidum TLS)
- P840 reaction center 17 kda protein (16 kDa, Protein from Chlorobaculum tepidum TLS)
- Chlorophyll a ester (891 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriochlorophyll a protein (40 kDa, Protein from Chlorobaculum tepidum TLS)
- 2-[(1e,3e,5e,7e,9e,11e,13e,15e,17e,19e)-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,4-trimethyl-benzene (532 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Psce (6 kDa, Protein from Chlorobaculum tepidum TLS)
- [(2r,3s,4s,5r,6r)-6-[(10e,12e,14e)-2,6,10,14,19,23-hexamethyl-25-(2,3,6-trimethylphenyl)pentacosa-6,8,10,12,14,16,18,20,22,24-decaen-2-yl]oxy-3,4,5-tris(oxidanyl)oxan-2-yl]methyl dodecanoate (895 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosynthetic assembly (rc-fmo2) (504 kDa, Complex from Chlorobaculum tepidum TLS)
- Bacteriochlorophyll a isomer (911 Da, Ligand)
- Photosystem p840 reaction center iron-sulfur protein (23 kDa, Protein from Chlorobaculum tepidum TLS)
Rba sphaeroides WT RC-LH1 monomer
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 7vny
Q-score: 0.633
Cao P, Bracun L, Yamagata A, Christianson BM, Negami T, Zou B, Terada T, Canniffe DP, Shirouzu M, Li M, Liu LN
Nat Commun (2022) 13 pp. 1977-1977 [ Pubmed: 35418573 DOI: doi:10.1038/s41467-022-29563-3 ]
- Rsp_7571 protein-y pufy (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rhodobacter sphaeroides wt rc-lh1 monomer (Complex from Rhodobacter sphaeroides 2.4.1)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe (ii) ion (55 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Bacteriopheophytin b (887 Da, Ligand)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Rba sphaeroides PufY-KO RC-LH1 dimer type-1
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 7va9
Q-score: 0.517
Cao P, Bracun L, Yamagata A, Christianson BM, Negami T, Zou B, Terada T, Canniffe DP, Shirouzu M, Li M, Liu LN
Nat Commun (2022) 13 pp. 1977-1977 [ Pubmed: 35418573 DOI: doi:10.1038/s41467-022-29563-3 ]
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe (ii) ion (55 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rhodobacter sphaeroides pufy-ko rc-lh1 dimer type-1 (Complex from Rhodobacter sphaeroides 2.4.1)
- Bacteriopheophytin b (887 Da, Ligand)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Rba sphaeroides PufY-KO RC-LH1 dimer type-2
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 7vb9
Q-score: 0.456
Cao P, Bracun L, Yamagata A, Christianson BM, Negami T, Zou B, Terada T, Canniffe DP, Shirouzu M, Li M, Liu LN
Nat Commun (2022) 13 pp. 1977-1977 [ Pubmed: 35418573 DOI: doi:10.1038/s41467-022-29563-3 ]
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe (ii) ion (55 Da, Ligand)
- Rhodobacter sphaeroides pufy-ko rc-lh1 dimer type-2 (Complex from Rhodobacter sphaeroides 2.4.1)
- Bacteriochlorophyll a (911 Da, Ligand)
- Spheroidene (568 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Cardiolipin (1 kDa, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)
Rba sphaeroides PufY-KO RC-LH1 monomer
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 7vnm
Q-score: 0.591
Cao P, Bracun L, Yamagata A, Christianson BM, Negami T, Zou B, Terada T, Canniffe DP, Shirouzu M, Li M, Liu LN
Nat Commun (2022) 13 pp. 1977-1977 [ DOI: doi:10.1038/s41467-022-29563-3 Pubmed: 35418573 ]
- Light-harvesting protein b-875 beta chain (5 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Rhodobacter sphaeroides pufy-ko rc-lh1 monomer (Complex from Rhodobacter sphaeroides 2.4.1)
- Reaction center protein l chain (31 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Reaction center protein h chain (28 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Spheroidene (568 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Fe (ii) ion (55 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Intrinsic membrane protein pufx (9 kDa, Protein from Cereibacter sphaeroides 2.4.1)
- Ubiquinone-10 (863 Da, Ligand)
- 1,2-diacyl-sn-glycero-3-phosphocholine (790 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Light-harvesting protein b-875 alpha chain (6 kDa, Protein from Cereibacter sphaeroides 2.4.1)