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)
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 [ Pubmed: 37399405 DOI: doi:10.1073/pnas.2220477120 ]
- Light-harvesting protein b-800/850 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Light-harvesting protein b800-820 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
- 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)
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 [ Pubmed: 37399405 DOI: doi:10.1073/pnas.2220477120 ]
- Light-harvesting protein b-800/850 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Light-harvesting protein b800-820 alpha chain (6 kDa, Protein from Magnetospirillum molischianum)
- Light-harvesting protein b-800/850 beta 1 chain (4 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)
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 [ Pubmed: 36693097 DOI: doi:10.1073/pnas.2216734120 ]
- Cytochrome c (22 kDa, Protein from Chlorobaculum tepidum TLS)
- [(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)
- Photosystem p840 reaction center, large subunit (81 kDa, Protein from Chlorobaculum tepidum TLS)
- Water (18 Da, Ligand)
- P840 reaction center 17 kda protein (16 kDa, Protein from Chlorobaculum tepidum TLS)
- 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)
- Chlorophyll a (893 Da, Ligand)
- Photosystem p840 reaction center (490 kDa, Complex from Chlorobaculum tepidum TLS)
- 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)
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 ]
- Fe (iii) ion (55 Da, Ligand)
- Reaction center protein m chain (34 kDa, Protein from Rhodobacter capsulatus)
- Reaction center protein l chain (31 kDa, Protein from Rhodobacter capsulatus)
- Spheroidene (568 Da, Ligand)
- Rc-lh1-pufx photosynthetic core complex from rba. capsulatus (Complex from Rhodobacter capsulatus)
- Intrinsic membrane protein pufx (8 kDa, Protein from Rhodobacter capsulatus)
- Reaction center protein h chain (28 kDa, Protein from Rhodobacter capsulatus)
- Bacteriochlorophyll a (911 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Lh1 beta chain (5 kDa, Protein from Rhodobacter capsulatus)
- 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)
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 ]
- Cytochrome c (22 kDa, Protein from Chlorobaculum tepidum TLS)
- Ric1 protein (6 kDa, Protein from Chlorobaculum tepidum TLS)
- P840 reaction center 17 kda protein (16 kDa, Protein from Chlorobaculum tepidum TLS)
- Iron/sulfur cluster (351 Da, Ligand)
- Chlorophyll a ester (891 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Bacteriochlorophyll a protein (40 kDa, Protein from Chlorobaculum tepidum TLS)
- Cardiolipin (1 kDa, Ligand)
- Photosystem p840 reaction center iron-sulfur protein (23 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)
- Unkown protein (4 kDa, Protein from Chlorobaculum tepidum TLS)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Gsbrc-2fmo complex (Complex from Chlorobaculum tepidum TLS)
- 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, large subunit (81 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 ]
- (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 m chain (36 kDa, Protein from Rhodopila globiformis)
- Photosynthetic reaction center h subunit (28 kDa, Protein from Rhodopila globiformis)
- Heme c (618 Da, Ligand)
- Bacteriopheophytin a (889 Da, Ligand)
- Ubiquinone-10 (863 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Cardiolipin (1 kDa, Ligand)
- Photosynthetic reaction center cytochrome c subunit (37 kDa, Protein from Rhodopila globiformis)
- Menaquinone-9 (785 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Light-harvesting protein lh1 gamma-like (2 kDa, Protein from Rhodopila globiformis)
- Light-harvesting protein (7 kDa, Protein from Rhodopila globiformis)
- Water (18 Da, Ligand)
- Photosynthetic lh1-rc complex from the purple phototrophic bacterium rhodopila globiformis (400 kDa, Complex from Rhodopila globiformis)
- (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)
- Light-harvesting protein (7 kDa, Protein from Rhodopila globiformis)
- Reaction center protein l chain (30 kDa, Protein from Rhodopila globiformis)
- 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)