Cryo-EM structure of E. coli cytochrome bo3 quinol oxidase assembled in peptidiscs
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8qqk
Q-score: 0.594
Gao Y, Zhang Y, Hakke S, Mohren R, Sijbers LJPM, Peters PJ, Ravelli RBG
Biochim Biophys Acta Bioenerg (2024) 1865 pp. 149045-149045 [ Pubmed: 38614453 DOI: doi:10.1016/j.bbabio.2024.149045 ]
- Copper (ii) ion (63 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 3 (22 kDa, Protein from Escherichia coli BL21(DE3))
- Cytochrome bo(3) ubiquinol oxidase subunit 4 (12 kDa, Protein from Escherichia coli BL21(DE3))
- Cytochrome bo(3) ubiquinol oxidase subunit 2 (34 kDa, Protein from Escherichia coli BL21(DE3))
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
- Heme o (838 Da, Ligand)
- Cytochrome bo(3) ubiquinol oxidase subunit 1 (74 kDa, Protein from Escherichia coli BL21(DE3))
- Cytochrome bo3 quinol oxidase (144 kDa, Complex from Escherichia coli)
- 1,2-distearoyl-sn-glycerophosphoethanolamine (748 Da, Ligand)
2.43 A Mycobacterium marinum EspB.
Resolution: 2.43 Å
EM Method: Single-particle
Fitted PDBs: 7p0z
Q-score: 0.648
Gijsbers A, Vinciauskaite V, Siroy A, Gao Y, Tria G, Mathew A, Sanchez-Puig N, Lopez-Iglesias C, Peters PJ, Ravelli RBG
Curr Res Struct Biol (2021) 3 pp. 153-164 [ Pubmed: 34337436 DOI: doi:10.1016/j.crstbi.2021.06.001 ]
- Heptamer of espb (210 kDa, Complex from Mycobacterium marinum)
- Esx-1 secretion-associated protein espb (31 kDa, Protein from Mycobacterium marinum (strain ATCC BAA-535 / M))
2.29 A Mycobacterium tuberculosis EspB.
Resolution: 2.29 Å
EM Method: Single-particle
Fitted PDBs: 7p13
Q-score: 0.672
Gijsbers A, Vinciauskaite V, Siroy A, Gao Y, Tria G, Mathew A, Sanchez-Puig N, Lopez-Iglesias C, Peters PJ, Ravelli RBG
Curr Res Struct Biol (2021) 3 pp. 153-164 [ Pubmed: 34337436 DOI: doi:10.1016/j.crstbi.2021.06.001 ]
- Esx-1 secretion-associated protein espb (31 kDa, Protein from Mycobacterium tuberculosis H37RV)
- Heptamer of espb (220 kDa, Complex from Mycobacterium tuberculosis H37RV)
Cryo-EM structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6iww
Q-score: 0.434
Xu X, Shi H, Gong X, Chen P, Gao Y, Zhang X, Xiang S
eLife (2020) 9 [ DOI: doi:10.7554/eLife.53853 Pubmed: 32459174 ]
- Oxaloacetate decarboxylase beta chain (44 kDa, Protein from Salmonella enterica subsp. enterica serovar Typhimurium)
- Probable oxaloacetate decarboxylase gamma chain (11 kDa, Protein from Salmonella enterica subsp. enterica serovar Typhimurium)
- Dodecyl-beta-d-maltoside (510 Da, Ligand)
- The oxaloacetate decarboxylase beta-gamma sub-complex (Complex from Salmonella enterica subsp. enterica serovar Typhimurium)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6n7w
Q-score: 0.324
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
- Dna (25-mer) (7 kDa, DNA from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Dna (77-mer) (23 kDa, DNA from Enterobacteria phage T7)
- Trxa (11 kDa, Protein from Escherichia coli)
- D5ae7a mutant gp5 dna polymerase complexed with trx, fork dna, and incoming dttp (from gp4-gp5 leading-strand complexes) (Complex from Enterobacteria phage T7)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6n9u
Q-score: 0.477
Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W
Science (2019) 363 [ Pubmed: 30679383 DOI: doi:10.1126/science.aav7003 ]
- Dna primase/helicase (62 kDa, Protein from Enterobacteria phage T7)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Rna (5'-r(*ap*cp*cp*ap*g)-d(p*(doc))-3') (1 kDa, RNA from Enterobacteria phage T7)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed dna polymerase (79 kDa, Protein from Enterobacteria phage T7)
- Gp5 dna polymerase and two gp4 primase subunits complexed with trx, rna/dna hybrid, and incoming dttp (from gp4-gp5 lagging-strand complex lags1) (Complex from Enterobacteria phage T7)
- Dna (44-mer) (13 kDa, DNA from Enterobacteria phage T7)