Structure of PsCas9 in complex with gRNA and DNA in product state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8umf
Q-score: 0.526
To Be Published
- Dna (80-mer) (24 kDa, DNA from synthetic construct)
- Cas9 (168 kDa, Protein from Parasutterella secunda)
- Rna (121-mer) (41 kDa, RNA from synthetic construct)
- Pscas9 in with grna and dsdna, product state (211 kDa, Complex from Parasutterella secunda)
- Dna (80-mer) (24 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 8t7s
Q-score: 0.408
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ DOI: doi:10.1038/s41467-024-47830-3 Pubmed: 38688943 ]
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Ts (16 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Dna-mediated dimer of spry-cas9 ternary complexes each with grna (423 kDa, Complex from Streptococcus pyogenes)
- Water (18 Da, Ligand)
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 ]
- Guide rna (6 kDa, RNA from synthetic construct)
- Tir-apaz (53 kDa, Protein from Maribacter polysiphoniae)
- Target dna (7 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Symmetric dimer of mapsparta bound with grna/tdna hybrid (Complex from Maribacter polysiphoniae)
- Short pago (58 kDa, Protein from Maribacter polysiphoniae)
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 ]
- Target dna (7 kDa, DNA from Maribacter polysiphoniae)
- Asymmetric dimer of mapsparta bound with grna/tdna hybrid (Complex from Maribacter polysiphoniae)
- Guide rna (6 kDa, RNA from Maribacter polysiphoniae)
- Tir-apaz (53 kDa, Protein from Maribacter polysiphoniae)
- Magnesium ion (24 Da, Ligand)
- Short pago (58 kDa, Protein 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 [ Pubmed: 37410820 DOI: doi:10.1126/science.adg4725 ]
- Rna-editing substrate-binding complex protein 3 (resc3) (53 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 1 (resc1) (52 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 4 (resc4) (120 kDa, Protein from Trypanosoma brucei)
- Grna (14 kDa, RNA from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 2 (resc2) (55 kDa, Protein from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 5 (resc5) (43 kDa, Protein from Trypanosoma brucei)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Resc5-tagged isolate without rnase treatment (Complex from Trypanosoma brucei)
- Rna-editing substrate-binding complex protein 6 (resc6) (57 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 [ Pubmed: 37410820 DOI: doi:10.1126/science.adg4725 ]
- Resc5-tagged isolate with rnase treatment (Complex from Trypanosoma brucei)
- Mrna (5 kDa, RNA from Trypanosoma brucei)
- Grna (4 kDa, RNA from Trypanosoma brucei)
- Rxlr effector protein (18 kDa, Protein from Trypanosoma brucei)
- Mitochondrial rna binding complex 1 subunit (61 kDa, Protein from Trypanosoma brucei)
- Rap domain-containing protein (60 kDa, Protein from Trypanosoma brucei)
- Phytanoyl-coa dioxygenase family protein (41 kDa, Protein from Trypanosoma brucei)
- Mitochondrial rna binding protein (34 kDa, Protein from Trypanosoma brucei)
- Rap domain-containing protein (57 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 [ Pubmed: 37410820 DOI: doi:10.1126/science.adg4725 ]
- Grna (4 kDa, RNA from Trypanosoma brucei)
- Rxlr effector protein (18 kDa, Protein from Trypanosoma brucei)
- Mitochondrial rna binding complex 1 subunit (61 kDa, Protein from Trypanosoma brucei)
- Rap domain-containing protein (60 kDa, Protein from Trypanosoma brucei)
- Mrna (6 kDa, RNA from Trypanosoma brucei)
- Resc5-tagged isolate without rnase treatment (Complex from Trypanosoma brucei)
- Phytanoyl-coa dioxygenase family protein (41 kDa, Protein from Trypanosoma brucei)
- Mitochondrial rna binding protein (34 kDa, Protein from Trypanosoma brucei)
- Rap domain-containing protein (57 kDa, Protein from Trypanosoma brucei)
Cryo-EM structure of TIR-APAZ/Ago-gRNA-DNA complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8i87
Q-score: 0.53
Wang X, Li X, Yu G, Zhang L, Zhang C, Wang Y, Liao F, Wen Y, Yin H, Liu X, Wei Y, Li Z, Deng Z, Zhang H
Cell Res (2023) 33 pp. 699-711 [ DOI: doi:10.1038/s41422-023-00839-7 Pubmed: 37311833 ]
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
- Dna (5'-d(p*tp*ap*tp*ap*cp*ap*ap*cp*cp*tp*ap*cp*tp*ap*cp*cp*tp*cp*a)-3') (5 kDa, DNA from Maribacter polysiphoniae)
- Tir-apaz/ago-grna-dna complex (Complex from Maribacter polysiphoniae)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*a)-3') (6 kDa, RNA from Maribacter polysiphoniae)
Cryo-EM structure of Thermus thermophilus reiterative transcription complex with 11nt oligo-G RNA
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7rdq
Q-score: 0.516
Liu Y, Yu L, Pukhrambam C, Winkelman JT, Firlar E, Kaelber JT, Zhang Y, Nickels BE, Ebright RH
PNAS (2022) 119 [ Pubmed: 35082149 DOI: doi:10.1073/pnas.2115746119 ]
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit beta (125 kDa, Protein from Thermus thermophilus HB8)
- Reiterative transcription initiation complex with 11nt oligo-g rna (425 kDa, Complex from Thermus thermophilus HB8)
- Rna polymerase sigma factor siga (48 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit beta' (170 kDa, Protein from Thermus thermophilus HB8)
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Thermus thermophilus HB8)
- Rna (5'-r(p*gp*gp*gp*gp*gp*gp*gp*gp*gp*gp*g)-3') (3 kDa, RNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna (31-mer) nontemplate strand (10 kDa, DNA from synthetic construct)
- Dna-directed rna polymerase subunit alpha (35 kDa, Protein from Thermus thermophilus HB8)
- Dna (31-mer) template strand (10 kDa, DNA from synthetic construct)