Cryo-EM structure of the ISFba1 TnpB-reRNA-dsDNA complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8iaz
Q-score: 0.548
Ren K, Zhou F, Zhang F, Yin M, Zhu Y, Wang S, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z
Cell Res (2024) 34 pp. 370-385 [ DOI: doi:10.1038/s41422-024-00952-1 Pubmed: 38575718 ]
- The complex of protein with grna and target dna (Complex from Firmicutes bacterium AM43-11BH)
- Dna (5'-d(p*cp*cp*ap*tp*tp*ap*gp*gp*ap*gp*cp*tp*gp*ap*tp*g)-3') (4 kDa, DNA from Firmicutes bacterium AM43-11BH)
- Transposase (44 kDa, Protein from Firmicutes bacterium AM43-11BH)
- Dna (5'-d(p*ap*cp*ap*tp*gp*gp*ap*cp*cp*ap*tp*cp*ap*gp*cp*tp*cp*cp*tp*ap*ap*tp*gp*g)-3') (7 kDa, DNA from Firmicutes bacterium AM43-11BH)
- Zinc ion (65 Da, Ligand)
- Rna (207-mer) (66 kDa, RNA from Firmicutes bacterium AM43-11BH)
Symmetric dimer of MapSPARTA bound with gRNA/tDNA hybrid
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8sp0
Q-score: 0.33
Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM
Nature (2023) 621 pp. 154-161 [ Pubmed: 37494956 DOI: doi:10.1038/s41586-023-06456-z ]
- Magnesium ion (24 Da, Ligand)
- Guide rna (6 kDa, RNA from synthetic construct)
- Symmetric dimer of mapsparta bound with grna/tdna hybrid (Complex from Maribacter polysiphoniae)
- Short pago (58 kDa, Protein from Maribacter polysiphoniae)
- Tir-apaz (53 kDa, Protein from Maribacter polysiphoniae)
- Target dna (7 kDa, DNA from synthetic construct)
Asymmetric dimer of MapSPARTA bound with gRNA/tDNA hybrid
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8sp3
Q-score: 0.298
Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM
Nature (2023) 621 pp. 154-161 [ Pubmed: 37494956 DOI: doi:10.1038/s41586-023-06456-z ]
- Magnesium ion (24 Da, Ligand)
- Asymmetric dimer of mapsparta bound with grna/tdna hybrid (Complex from Maribacter polysiphoniae)
- Target dna (7 kDa, DNA from Maribacter polysiphoniae)
- Short pago (58 kDa, Protein from Maribacter polysiphoniae)
- Tir-apaz (53 kDa, Protein from Maribacter polysiphoniae)
- Guide rna (6 kDa, RNA from Maribacter polysiphoniae)
Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM
Nature (2023) 621 pp. 154-161 [ Pubmed: 37494956 DOI: doi:10.1038/s41586-023-06456-z ]
Monomeric MapSPARTA bound with guide RNA and target DNA hybrid
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 8squ
Q-score: 0.304
Shen Z, Yang XY, Xia S, Huang W, Taylor DJ, Nakanishi K, Fu TM
Nature (2023) 621 pp. 154-161 [ Pubmed: 37494956 DOI: doi:10.1038/s41586-023-06456-z ]
- Complex of mapsparta binding with grna tdna hybrid (Complex from Maribacter polysiphoniae)
- Magnesium ion (24 Da, Ligand)
- Target dna (7 kDa, DNA from Maribacter polysiphoniae)
- Short pago (58 kDa, Protein from Maribacter polysiphoniae)
- Tir-apaz (53 kDa, Protein from Maribacter polysiphoniae)
- Guide rna (6 kDa, RNA from Maribacter polysiphoniae)
Cryo-EM structure of RNase-untreated RESC-A in trypanosomal RNA editing
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8fn6
Q-score: 0.386
Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH
Science (2023) 381 pp. eadg4725-eadg4725 [ DOI: doi:10.1126/science.adg4725 Pubmed: 37410820 ]
- Rna-editing substrate-binding complex protein 2 (resc2) (55 kDa, Protein from Trypanosoma brucei)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Rna-editing substrate-binding complex protein 5 (resc5) (43 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 3 (resc3) (53 kDa, Protein from Trypanosoma brucei)
- Resc5-tagged isolate without rnase treatment (Complex from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 1 (resc1) (52 kDa, Protein from Trypanosoma brucei)
- Grna (14 kDa, RNA from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 6 (resc6) (57 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 4 (resc4) (120 kDa, Protein from Trypanosoma brucei)
Cryo-EM structure of RNase-treated RESC-C in trypanosomal RNA editing
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8fnc
Q-score: 0.533
Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH
Science (2023) 381 pp. eadg4725-eadg4725 [ DOI: doi:10.1126/science.adg4725 Pubmed: 37410820 ]
- Mitochondrial rna binding complex 1 subunit (61 kDa, Protein from Trypanosoma brucei)
- Mrna (5 kDa, RNA from Trypanosoma brucei)
- Rap domain-containing protein (57 kDa, Protein from Trypanosoma brucei)
- Grna (4 kDa, RNA from Trypanosoma brucei)
- Mitochondrial rna binding protein (34 kDa, Protein from Trypanosoma brucei)
- Rap domain-containing protein (60 kDa, Protein from Trypanosoma brucei)
- Rxlr effector protein (18 kDa, Protein from Trypanosoma brucei)
- Resc5-tagged isolate with rnase treatment (Complex from Trypanosoma brucei)
- Phytanoyl-coa dioxygenase family protein (41 kDa, Protein from Trypanosoma brucei)
Cryo-EM structure of RNase-untreated RESC-C in trypanosomal RNA editing
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8fnf
Q-score: 0.448
Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH
Science (2023) 381 pp. eadg4725-eadg4725 [ DOI: doi:10.1126/science.adg4725 Pubmed: 37410820 ]
- Mitochondrial rna binding complex 1 subunit (61 kDa, Protein from Trypanosoma brucei)
- Grna (4 kDa, RNA from Trypanosoma brucei)
- Resc5-tagged isolate without rnase treatment (Complex from Trypanosoma brucei)
- Mrna (6 kDa, RNA from Trypanosoma brucei)
- Mitochondrial rna binding protein (34 kDa, Protein from Trypanosoma brucei)
- Rap domain-containing protein (60 kDa, Protein from Trypanosoma brucei)
- Rxlr effector protein (18 kDa, Protein from Trypanosoma brucei)
- Rap domain-containing protein (57 kDa, Protein from Trypanosoma brucei)
- Phytanoyl-coa dioxygenase family protein (41 kDa, Protein from Trypanosoma brucei)
Cryo-EM structure of RNase-treated RESC-B in trypanosomal RNA editing
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8fni
Q-score: 0.443
Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH
Science (2023) 381 pp. eadg4725-eadg4725 [ DOI: doi:10.1126/science.adg4725 Pubmed: 37410820 ]
- Rna-editing substrate-binding complex protein 7 (resc7) (18 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 13 (resc13) (32 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 11 (resc11) (103 kDa, Protein from Trypanosoma brucei)
- Mrna (6 kDa, RNA from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 5 (resc5) (43 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 9 (resc9) (96 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 10 (resc10) (60 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 14 (resc14) (41 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 8 (resc8) (61 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 6 (resc6) (57 kDa, Protein from Trypanosoma brucei)
- Resc5-tagged isolate with rnase treatment (Complex from Trypanosoma brucei)
- Grna (4 kDa, RNA from Trypanosoma brucei)
Cryo-EM structure of RNase-untreated RESC-B in trypanosomal RNA editing
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8fnk
Q-score: 0.37
Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH
Science (2023) 381 pp. eadg4725-eadg4725 [ DOI: doi:10.1126/science.adg4725 Pubmed: 37410820 ]
- Grna (13 kDa, RNA from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 7 (resc7) (18 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 13 (resc13) (32 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 8 (resc8) (61 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 11 (resc11) (103 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 5 (resc5) (43 kDa, Protein from Trypanosoma brucei)
- Resc5-tagged isolate without rnase treatment (Complex from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 9 (resc9) (96 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 10 (resc10) (60 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 14 (resc14) (41 kDa, Protein from Trypanosoma brucei)
- Mrna (15 kDa, RNA from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 6 (resc6) (57 kDa, Protein from Trypanosoma brucei)