Cryo-EM structure of photosynthetic LH1' complex of Roseospirillum parvum
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8zjw
Q-score: 0.699
Wang XP, Wang GL, Fu Y, Minamino A, Zou MJ, Ma F, Xu B, Wang-Otomo ZY, Kimura Y, Madigan MT, Overmann J, Yu LJ
Commun Biol (2024) 7 pp. 1658-1658 [ Pubmed: 39702771 DOI: doi:10.1038/s42003-024-07354-4 ]
- Lh1 prime complex (Complex from Roseospirillum parvum)
- Bacteriochlorophyll a (911 Da, Ligand)
- Beta subunit of light-harvesting 1 complex (7 kDa, Protein from Roseospirillum parvum)
- Alpha subunit of light-harvesting 1 complex (7 kDa, Protein from Roseospirillum parvum)
- Spirilloxanthin (596 Da, Ligand)
Cryo-EM structure of photosynthetic LH1-RC core complex of Roseospirillum parvum
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8zk2
Q-score: 0.637
Wang XP, Wang GL, Fu Y, Minamino A, Zou MJ, Ma F, Xu B, Wang-Otomo ZY, Kimura Y, Madigan MT, Overmann J, Yu LJ
Commun Biol (2024) 7 pp. 1658-1658 [ Pubmed: 39702771 DOI: doi:10.1038/s42003-024-07354-4 ]
- 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)
- Heme c (618 Da, Ligand)
- Photosynthetic reaction center cytochrome c subunit (39 kDa, Protein from Roseospirillum parvum)
- Bacteriochlorophyll a (911 Da, Ligand)
- Beta subunit of light-harvesting 1 complex (7 kDa, Protein from Roseospirillum parvum)
- Magnesium ion (24 Da, Ligand)
- Menaquinone 8 (717 Da, Ligand)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- Photosynthetic reaction center h subunit (27 kDa, Protein from Roseospirillum parvum)
- Alpha subunit of light-harvesting 1 complex (7 kDa, Protein from Roseospirillum parvum)
- Bacteriopheophytin a (889 Da, Ligand)
- Octadecane (254 Da, Ligand)
- Spirilloxanthin (596 Da, Ligand)
- Lh1-rc core complex (Complex from Roseospirillum parvum)
- Reaction center protein l chain (30 kDa, Protein from Roseospirillum parvum)
- Reaction center protein m chain (35 kDa, Protein from Roseospirillum parvum)
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 ]
- Dodecane (170 Da, Ligand)
- Lh1 beta polypeptide (5 kDa, Protein from Thermochromatium tepidum)
- Calcium ion (40 Da, Ligand)
- Bacteriochlorophyll a (911 Da, Ligand)
- Lh1 alpha polypeptide (7 kDa, Protein from Thermochromatium tepidum)
- Spirilloxanthin (596 Da, Ligand)
- Lh1 complex (Complex from Thermochromatium tepidum)
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)
The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric apo state
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8k0p
Q-score: 0.444
The Anoxybacillus pushchinoensis ORF-less Group IIC Intron DR1 at symmetric pre-cleavage state
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8k0q
Q-score: 0.365
Liu ZX, Zhang S, Zhu HZ, Chen ZH, Yang Y, Li LQ, Lei Y, Liu Y, Li DY, Sun A, Li CP, Tan SQ, Wang GL, Shen JY, Jin S, Gao C, Liu JG
Science (2024) 383 pp. eadh4859-eadh4859 [ DOI: doi:10.1126/science.adh4859 Pubmed: 38301022 ]
- Rna (Complex)
- The anoxybacillus pushchinoensis orf-less group iic intron hyer1 at symmetric pre-cleavage state (Complex from Anoxybacillus pushchinoensis)
- Dna (Complex)
- Dna (2 kDa, DNA from Anoxybacillus pushchinoensis)
- Magnesium ion (24 Da, Ligand)
- Rna (542-mer) (205 kDa, RNA from Anoxybacillus pushchinoensis)