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)
BG505.MD39TS Env trimer in complex with Fab from antibody C05
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 7sq1
Q-score: 0.406
Xu Z, Walker S, Wise MC, Chokkalingam N, Purwar M, Moore A, Tello-Ruiz E, Wu Y, Majumdar S, Konrath KM, Kulkarni A, Tursi NJ, Zaidi FI, Reuschel EL, Patel I, Obeirne A, Du J, Schultheis K, Gites L, Smith T, Mendoza J, Broderick KE, Humeau L, Pallesen J, Weiner DB, Kulp DW
Nat Commun (2022) 13 pp. 695-695 [ DOI: doi:10.1038/s41467-022-28363-z Pubmed: 35121758 ]
- C05 fab light chain (12 kDa, Protein from Mus musculus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Transmembrane protein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- C05 fab heavy chain (13 kDa, Protein from Mus musculus)
- Bg505.md39ts env trimer in complex with fab from antibody c05 (410 kDa, Complex)
- Envelope glycoprotein gp160 (52 kDa, Protein from Human immunodeficiency virus 1)
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)
Cas9 bound to 12-14MM DNA, 60 min time-point, kinked conformation
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 7s4v
Q-score: 0.448
Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW
Nature (2022) 603 pp. 343-347 [ DOI: doi:10.1038/s41586-022-04470-1 Pubmed: 35236982 ]
- Grna (31 kDa, RNA from synthetic construct)
- Cas9 bound to 12-14mm dna, 60 min time-point, kinked conformation (Complex from Streptococcus pyogenes)
- Ts (10 kDa, DNA from synthetic construct)
- Nts (9 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
Cas9:gRNA in complex with 18-20MM DNA, 1 minute time-point, kinked active conformation
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 7s4x
Q-score: 0.551
Bravo JPK, Liu MS, Hibshman GN, Dangerfield TL, Jung K, McCool RS, Johnson KA, Taylor DW
Nature (2022) 603 pp. 343-347 [ Pubmed: 35236982 DOI: doi:10.1038/s41586-022-04470-1 ]
- Nts (10 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Ts (4 kDa, DNA from synthetic construct)
- Water (18 Da, Ligand)
- Ts (6 kDa, DNA from synthetic construct)
- Grna (31 kDa, RNA from synthetic construct)
- Cas9 bound to 18-20mm dna, 1 min time-point, kinked active conformation (Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)