Architecture of the spinach plastid-encoded RNA polymerase
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 8xzv
Q-score: 0.444
Wang T, Wang GL, Fang Y, Zhang Y, Peng W, Zhou Y, Zhang A, Yu LJ, Lu C
Nat Commun (2024) 15 pp. 9838-9838 [ DOI: doi:10.1038/s41467-024-54266-2 Pubmed: 39537621 ]
- Fructokinase-like 2, chloroplastic isoform x2 (65 kDa, Protein from Spinacia oleracea)
- Dna-directed rna polymerase subunit beta' (78 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 7 (19 kDa, Protein from Spinacia oleracea)
- Ptac18 (17 kDa, Protein from Spinacia oleracea)
- Superoxide dismutase (31 kDa, Protein from Spinacia oleracea)
- Mure (85 kDa, Protein from Spinacia oleracea)
- Superoxide dismutase (31 kDa, Protein from Spinacia oleracea)
- Dna-directed rna polymerase subunit alpha (38 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 12 (59 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 14 isoform x2 (56 kDa, Protein from Spinacia oleracea)
- Ptac3 (101 kDa, Protein from Spinacia oleracea)
- Fe (iii) ion (55 Da, Ligand)
- Dna-directed rna polymerase subunit beta (121 kDa, Protein from Spinacia oleracea)
- Dna-directed rna polymerase subunit beta'' (154 kDa, Protein from Spinacia oleracea)
- Protein plastid transcriptionally active 10 (80 kDa, Protein from Spinacia oleracea)
- Spinach plastid-encoded rna polymerase (960 kDa, Complex from Spinacia oleracea)
- Ptac6 (37 kDa, Protein from Spinacia oleracea)
- Fructokinase-like 1, chloroplastic (53 kDa, Protein from Spinacia oleracea)
- Thioredoxin-like protein citrx, chloroplastic (20 kDa, Protein from Spinacia oleracea)
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)
Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris
Qi CH, Wang GL, Wang FF, Wang J, Wang XP, Zou MJ, Ma F, Madigan MT, Kimura Y, Wang-Otomo ZY, Yu LJ
J Integr Plant Biol (2024) 66 pp. 2262-2272 [ DOI: doi:10.1111/jipb.13628 Pubmed: 38411333 ]
- (1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate (749 Da, Ligand)
- Reaction center protein m chain (36 kDa, Protein from Halorhodospira halochloris)
- Heme c (618 Da, Ligand)
- Trans-geranyl bacteriopheophytin b (885 Da, Ligand)
- Trans-geranyl 8-vinyl-bacteriochlorophyll b (907 Da, Ligand)
- Beta subunit of light-harvesting 1 (9 kDa, Protein from Halorhodospira halochloris)
- Ubiquinone-8 (727 Da, Ligand)
- Photosynthetic reaction center h subunit (31 kDa, Protein from Halorhodospira halochloris)
- Reaction center protein l chain (31 kDa, Protein from Halorhodospira halochloris)
- Menaquinone 8 (717 Da, Ligand)
- Lycopene (536 Da, Ligand)
- Antenna complex alpha/beta subunit domain-containing protein (7 kDa, Protein from Halorhodospira halochloris)
- Rc-lh core complex (Complex from Halorhodospira halochloris)
- Photosynthetic reaction center cytochrome c subunit (41 kDa, Protein from Halorhodospira halochloris)
- Light-harvesting lhi (7 kDa, Protein from Halorhodospira halochloris)
- Trans-geranyl bacteriochlorophyll b (907 Da, Ligand)
- Antenna complex alpha/beta subunit domain-containing protein (12 kDa, Protein from Halorhodospira halochloris)
- 2-o-octyl-beta-d-glucopyranose (292 Da, Ligand)
- Fe (iii) ion (55 Da, Ligand)
- Reaction center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
- Gamma subunit of light-harvesting 1 (3 kDa, Protein from Halorhodospira halochloris)
- Cardiolipin (1 kDa, Ligand)
- Di-palmitoyl-3-sn-phosphatidylethanolamine (691 Da, Ligand)
- Reactin center small polypeptide (3 kDa, Protein from Halorhodospira halochloris)
- Unknown ligand (909 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 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)