Cryo-EM structure of CasLambda (Cas12l) bound to crRNA and DNA
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8dc2
Q-score: 0.491
Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA
Cell (2022) 185 pp. 4574-4586.e16 [ Pubmed: 36423580 DOI: doi:10.1016/j.cell.2022.10.020 ]
- Rna (51-mer) (16 kDa, RNA from uncultured virus)
- Dna ts (14 kDa, DNA from uncultured virus)
- Caslambda (87 kDa, Protein from uncultured virus)
- Dna nts (14 kDa, DNA from uncultured virus)
- Caslambda-crrna-dsdna ternary structure (Complex from uncultured virus)
PlmCasX-sgRNAv1-dsDNA ternary complex at ts loading state
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7waz
Q-score: 0.246
Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG
Mol Cell (2022) 82 pp. 1199-1209.e6 [ DOI: doi:10.1016/j.molcel.2022.02.002 Pubmed: 35219382 ]
- Plmcasx-sgrnav1-dsdna ternary complex at nts loading state (Complex from Planctomycetes bacterium)
- Rna (115-mer) (39 kDa, RNA from Planctomycetes bacterium)
- Ts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Plmcasx (Complex from Planctomycetes bacterium)
- Nts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Dna (Complex from Planctomycetes bacterium)
- Dplmcasx (112 kDa, Protein from Planctomycetes bacterium)
- Rna (Complex)
PlmCasX-sgRNAv1-dsDNA ternary complex at nts loading state with flexible H2 domain
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7wb0
Q-score: 0.374
Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG
Mol Cell (2022) 82 pp. 1199-1209.e6 [ DOI: doi:10.1016/j.molcel.2022.02.002 Pubmed: 35219382 ]
- Plmcasx (Complex)
- Ts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Rna (115-mer) (39 kDa, RNA from Planctomycetes bacterium)
- Dplmcasx (112 kDa, Protein from Planctomycetes bacterium)
- Nts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Rna (Complex from Planctomycetes bacterium)
- Dna (Complex from Planctomycetes bacterium)
- Plmcasx-sgrnav1-dsdna ternary complex at nts loading state (Complex from Planctomycetes bacterium)
PlmCasX-sgRNAv2-dsDNA ternary complex at nts loading state
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7wb1
Q-score: 0.369
Tsuchida CA, Zhang S, Doost MS, Zhao Y, Wang J, O'Brien E, Fang H, Li CP, Li D, Hai ZY, Chuck J, Brotzmann J, Vartoumian A, Burstein D, Chen XW, Nogales E, Doudna JA, Liu JG
Mol Cell (2022) 82 pp. 1199-1209.e6 [ DOI: doi:10.1016/j.molcel.2022.02.002 Pubmed: 35219382 ]
- Plmcasx (Complex)
- Ts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Dplmcasx (112 kDa, Protein from Planctomycetes bacterium)
- Plmcasx-sgrnav2-dsdna ternary complex at nts loading state (Complex from Planctomycetes)
- Dsdna (Complex from Planctomycetes)
- Rna (121-mer) (38 kDa, RNA from Planctomycetes bacterium)
- Nts-dna (12 kDa, DNA from Planctomycetes bacterium)
- Sgrnav2 (Complex from Planctomycetes)
Cryo-EM structure of CasPhi-2 (Cas12j) bound to crRNA and DNA
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 7lys
Q-score: 0.517
Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA
Nat Struct Mol Biol (2021) 28 pp. 652-661 [ Pubmed: 34381246 DOI: doi:10.1038/s41594-021-00632-3 ]
- Cryo-em map of casphi bound to crrna and dna (124 kDa, Complex from Biggievirus Mos11)
- Crrna (14 kDa, RNA from Phage #D)
- Casphi-2 (86 kDa, Protein from Biggievirus Mos11)
- Ts-dna (12 kDa, DNA from Phage #D)
- Nts-dna (11 kDa, DNA from Phage #D)
Cryo-EM structure of CasPhi-2 (Cas12j) bound to crRNA and Phosphorothioate-DNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7lyt
Q-score: 0.524
Pausch P, Soczek KM, Herbst DA, Tsuchida CA, Al-Shayeb B, Banfield JF, Nogales E, Doudna JA
Nat Struct Mol Biol (2021) 28 pp. 652-661 [ Pubmed: 34381246 DOI: doi:10.1038/s41594-021-00632-3 ]
- Magnesium ion (24 Da, Ligand)
- Ts-dna (13 kDa, DNA from Biggievirus Mos11)
- Crrna (14 kDa, RNA from Biggievirus Mos11)
- Nts-dna* (13 kDa, DNA from Biggievirus Mos11)
- Zinc ion (65 Da, Ligand)
- Cryo-em map of casphi bound to crrna and phosphorothioate-dna in the presence of the nuclease magnesium cofactor (128 kDa, Complex from Biggievirus Mos11)
- Casphi (86 kDa, Protein from Biggievirus Mos11)
Structure of the SpCas9 DNA adenine base editor - ABE8e
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6vpc
Q-score: 0.37
Lapinaite A, Knott GJ, Palumbo CM, Lin-Shiao E, Richter MF, Zhao KT, Beal PA, Liu DR, Doudna JA
Science (2020) 369 pp. 566-571 [ Pubmed: 32732424 DOI: doi:10.1126/science.abb1390 ]
- Magnesium ion (24 Da, Ligand)
- Dna non-target strand (nts) (15 kDa, DNA from synthetic construct)
- Dna target strand (ts) (15 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas9 (157 kDa, Protein from Streptococcus pyogenes)
- Cas9 (spcas9) single-guide rna (sgrna) (26 kDa, RNA from Streptococcus pyogenes)
- Zinc ion (65 Da, Ligand)
- T-rna adenine deaminase a v8e (tada-8e) (24 kDa, Protein from Escherichia coli)
- Crispr-cas9 abe8e in a substrate-bound state (Complex from Streptococcus pyogenes)