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 ]
- [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)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cytochrome c domain-containing protein (15 kDa, Protein from Chloracidobacterium thermophilum)
- Heme c (618 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Psca (98 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)
- Pscd' (8 kDa, Protein from Chloracidobacterium thermophilum)
- [(2~{r})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (663 Da, Ligand)
- [(2s)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (649 Da, Ligand)
- Unknown ligand (663 Da, Ligand)
- Water (18 Da, Ligand)
- Psce (3 kDa, Protein from Chloracidobacterium thermophilum)
- Cytochrome c, mono-and diheme variants (22 kDa, Protein from Chloracidobacterium thermophilum)
- Calcium ion (40 Da, Ligand)
- Pscf (3 kDa, Protein from Chloracidobacterium thermophilum)
- Photosystem p840 reaction center iron-sulfur protein (8 kDa, Protein from Chloracidobacterium thermophilum)
- Cabrc complex, the larger form (Complex from Chloracidobacterium thermophilum)
- Pscg (4 kDa, Protein from Chloracidobacterium thermophilum)
- Undefined polypeptide (1 kDa, Protein from Chloracidobacterium thermophilum)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 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)
LH2-LH3 antenna in anti parallel configuration embedded in a nanodisc
Resolution: 8.2 Å
EM Method: Single-particle
Fitted PDBs: 7tuw
Q-score: 0.18
Wang D, Fiebig OC, Harris D, Toporik H, Ji Y, Chuang C, Nairat M, Tong AL, Ogren JI, Hart SM, Cao J, Sturgis JN, Mazor Y, Schlau-Cohen GS
PNAS (2023) 120 pp. e2220477120-e2220477120 [ DOI: doi:10.1073/pnas.2220477120 Pubmed: 37399405 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Light-harvesting protein b-800/850 beta 1 chain (5 kDa, Protein from Magnetospirillum molischianum)
- Light-harvesting protein b800-820 beta chain (5 kDa, Protein from Magnetospirillum molischianum)
- Lh2 and lh3 antennae (Complex from Magnetospirillum molischianum)
- Light-harvesting protein b-800/850 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
- Light-harvesting protein b800-820 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
LH2-LH3 antenna in parallel configuration embedded in a nanodisc
Resolution: 11.4 Å
EM Method: Single-particle
Fitted PDBs: 7tv3
Q-score: 0.084
Wang D, Fiebig OC, Harris D, Toporik H, Ji Y, Chuang C, Nairat M, Tong AL, Ogren JI, Hart SM, Cao J, Sturgis JN, Mazor Y, Schlau-Cohen GS
PNAS (2023) 120 pp. e2220477120-e2220477120 [ DOI: doi:10.1073/pnas.2220477120 Pubmed: 37399405 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Light-harvesting protein b800-820 beta chain (5 kDa, Protein from Magnetospirillum molischianum)
- Lh2 and lh3 antennae (Complex from Magnetospirillum molischianum)
- Light-harvesting protein b-800/850 beta 1 chain (4 kDa, Protein from Magnetospirillum molischianum)
- Light-harvesting protein b-800/850 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
- Light-harvesting protein b800-820 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
Cryo-EM structure of the whole photosynthetic complex from the green sulfur bacteria
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7z6q
Q-score: 0.493
Xie H, Lyratzakis A, Khera R, Koutantou M, Welsch S, Michel H, Tsiotis G
PNAS (2023) 120 pp. e2216734120-e2216734120 [ DOI: doi:10.1073/pnas.2216734120 Pubmed: 36693097 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- Water (18 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem p840 reaction center, large subunit (81 kDa, Protein from Chlorobaculum tepidum TLS)
- Bacteriochlorophyll a protein (40 kDa, Protein from Chlorobaculum tepidum TLS)
- Photosystem p840 reaction center iron-sulfur protein (23 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)
- [(2~{r})-2-hexadecanoyloxy-3-[(2~{s},3~{s},4~{r},5~{r},6~{s})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-propyl] hexadecanoate (731 Da, Ligand)
- Bacteriochlorophyll a isomer (911 Da, Ligand)
- Photosystem p840 reaction center (490 kDa, Complex from Chlorobaculum tepidum TLS)
- Chlorophyll a (893 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- P840 reaction center 17 kda protein (16 kDa, Protein from Chlorobaculum tepidum TLS)
- Cytochrome c (22 kDa, Protein from Chlorobaculum tepidum TLS)
Cryo-EM structure of RC-LH1-PufX photosynthetic core complex from Rba. capsulatus
Resolution: 2.589 Å
EM Method: Single-particle
Fitted PDBs: 8b64
Q-score: 0.639
Bracun L, Yamagata A, Christianson BM, Shirouzu M, Liu LN
Structure (2023) 31 pp. 318- [ Pubmed: 36738736 DOI: doi:10.1016/j.str.2023.01.006 ]
- Bacteriochlorophyll a (911 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter capsulatus)
- Light-harvesting protein b-870 alpha chain (6 kDa, Protein from Rhodobacter capsulatus)
- Intrinsic membrane protein pufx (8 kDa, Protein from Rhodobacter capsulatus)
- Spheroidene (568 Da, Ligand)
- Lh1 beta chain (5 kDa, Protein from Rhodobacter capsulatus)
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter capsulatus)
- Bacteriopheophytin a (889 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- Rc-lh1-pufx photosynthetic core complex from rba. capsulatus (Complex from Rhodobacter capsulatus)
- Reaction center protein h chain (28 kDa, Protein from Rhodobacter capsulatus)
- Fe (iii) ion (55 Da, Ligand)
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 ]
- [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)
- Photosynthetic reaction center subunit m (99 kDa, Protein from Chloracidobacterium thermophilum B)
- Bacteriochlorophyll a (911 Da, Ligand)
- Cytochrome c domain-containing protein (15 kDa, Protein from Chloracidobacterium thermophilum B)
- Heme c (618 Da, Ligand)
- Lycopene (536 Da, Ligand)
- [(2~{s})-2-[[(1~{r})-1,2-bis(13-methyltetradecanoyloxy)ethoxy]methyl]-3-oxidanyl-3-oxidanylidene-propyl]-trimethyl-azanium (671 Da, Ligand)
- [(2~{r})-2-[2-(methylamino)ethoxy-oxidanyl-phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (663 Da, Ligand)
- [(2s)-2-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-(13-methyltetradecanoyloxy)ethyl] 13-methyltetradecanoate (649 Da, Ligand)
- Pscf (3 kDa, Protein from Chloracidobacterium thermophilum B)
- Cabrc complex (Complex from Chloracidobacterium thermophilum)
- Water (18 Da, Ligand)
- Pscg (5 kDa, Protein from Chloracidobacterium thermophilum B)
- Cytochrome c, mono-and diheme variants (24 kDa, Protein from Chloracidobacterium thermophilum B)
- Calcium ion (40 Da, Ligand)
- Unknown ligand (671 Da, Ligand)
- Undefined polypeptide (1 kDa, Protein from Chloracidobacterium thermophilum)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a (893 Da, Ligand)
- Psce (3 kDa, Protein from Chloracidobacterium thermophilum B)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8gwa
Q-score: 0.541
Chen JH, Wang W, Wang C, Kuang T, Shen JR, Zhang X
J Integr Plant Biol (2023) 65 pp. 223-234 [ Pubmed: 36125941 DOI: doi:10.1111/jipb.13367 ]
- Chlorophyll a ester (891 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem p840 reaction center, large subunit (81 kDa, Protein from Chlorobaculum tepidum TLS)
- Bacteriochlorophyll a protein (40 kDa, Protein from Chlorobaculum tepidum TLS)
- Gsbrc-2fmo complex (Complex from Chlorobaculum tepidum TLS)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 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)
- Unkown protein (4 kDa, Protein from Chlorobaculum tepidum TLS)
- Ric1 protein (6 kDa, Protein from Chlorobaculum tepidum TLS)
- Photosystem p840 reaction center iron-sulfur protein (23 kDa, Protein from Chlorobaculum tepidum TLS)
- Iron/sulfur cluster (351 Da, Ligand)
- Bacteriochlorophyll a isomer (911 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- 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)
- Cardiolipin (1 kDa, Ligand)
- P840 reaction center 17 kda protein (16 kDa, Protein from Chlorobaculum tepidum TLS)
- Cytochrome c (22 kDa, Protein from Chlorobaculum tepidum TLS)
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)
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 [ DOI: doi:10.1038/s41467-022-33505-4 Pubmed: 36192412 ]
- Chlorophyll a ester (891 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Photosystem p840 reaction center, large subunit (81 kDa, Protein from Chlorobaculum tepidum TLS)
- Bacteriochlorophyll a protein (40 kDa, Protein from Chlorobaculum tepidum TLS)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem p840 reaction center iron-sulfur protein (23 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)
- Photosynthetic assembly (rc-fmo1) (370 kDa, Complex from Chlorobaculum tepidum TLS)
- Bacteriochlorophyll a isomer (911 Da, Ligand)
- 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-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- P840 reaction center 17 kda protein (16 kDa, Protein from Chlorobaculum tepidum TLS)
- Cytochrome c (22 kDa, Protein from Chlorobaculum tepidum TLS)