DNA bound type IV-A3 CRISPR effector complex from K. pneumoniae
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8rc2
Q-score: 0.518
Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P
Nat Commun (2024) 15 pp. 9306-9306 [ DOI: doi:10.1038/s41467-024-53778-1 Pubmed: 39468082 ]
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Target strand (ts)-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA from Klebsiella pneumoniae)
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein from Klebsiella pneumoniae)
- Non-target strand (nts)-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Type iv-a3 crispr-cas effector complex from klebsiella pneumoniae bound to crrna and target dna (332 kDa, Complex from Klebsiella pneumoniae)
DNA bound type IV-A1 CRISPR effector complex from P. oleovorans
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8rc3
Q-score: 0.522
Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P
Nat Commun (2024) 15 pp. 9306-9306 [ DOI: doi:10.1038/s41467-024-53778-1 Pubmed: 39468082 ]
- Crispr type aferr-associated protein csf1 (27 kDa, Protein from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf2 (37 kDa, Protein from Pseudomonas oleovorans)
- Target dna (Complex from Pseudomonas oleovorans)
- Target strand (ts) dna (18 kDa, DNA from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf3 (24 kDa, Protein from Pseudomonas oleovorans)
- Type iv-a1 crispr-cas effector complex from pseudomonas oleovorans bound to crrna and target dna (332 kDa, Complex)
- Zinc ion (65 Da, Ligand)
- Type iv-a1 crispr-cas effector complex from pseudomonas oleovorans bound to crrna (Complex from Pseudomonas oleovorans)
- Non-target strand (nts) dna (18 kDa, DNA from Pseudomonas oleovorans)
- Crrna (19 kDa, RNA from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf5 (25 kDa, Protein from Pseudomonas oleovorans)
DNA bound type IV-A1 CRISPR effector complex with the DinG helicase from P. oleovorans
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8rfj
Q-score: 0.402
Cepaite R, Klein N, Miksys A, Camara-Wilpert S, Ragozius V, Benz F, Skorupskaite A, Becker H, Zvejyte G, Steube N, Hochberg GKA, Randau L, Pinilla-Redondo R, Malinauskaite L, Pausch P
Nat Commun (2024) 15 pp. 9306-9306 [ DOI: doi:10.1038/s41467-024-53778-1 Pubmed: 39468082 ]
- Non-target strand (nts-) dna (18 kDa, DNA from Pseudomonas oleovorans)
- Target strand (ts-)dna (18 kDa, DNA from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf2 (37 kDa, Protein from Pseudomonas oleovorans)
- Target dna (Complex from Pseudomonas oleovorans)
- Type iv-a1 crispr-cas effector complex with the ding helicase from pseudomonas oleovorans bound to crrna and target dna (332 kDa, Complex)
- Crispr type aferr-associated protein csf3 (24 kDa, Protein from Pseudomonas oleovorans)
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf1 (27 kDa, Protein from Pseudomonas oleovorans)
- Type iv-a1 crispr-cas effector complex with the ding helicase from pseudomonas oleovorans bound to crrna (Complex from Pseudomonas oleovorans)
- Crrna (19 kDa, RNA from Pseudomonas oleovorans)
- Atp-dependent dna helicase ding (77 kDa, Protein from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf5 (25 kDa, Protein from Pseudomonas oleovorans)
SpCas9 with sgRNA and target DNA
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8g1i
Q-score: 0.392
To Be Published
- Crispr-associated endonuclease cas9 complex with sgrna and target dna (Complex from Streptococcus pyogenes)
- Dna e2_ts (12 kDa, DNA from Renilla reniformis)
- Crispr-associated endonuclease cas9/csn1 (160 kDa, Protein from Streptococcus pyogenes)
- Sgrna (31 kDa, RNA from Streptococcus pyogenes)
- Dna e2_nts (12 kDa, DNA from Renilla reniformis)
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)
Pol II-CSB-CSA-DDB1-UVSSA (Structure1)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7oo3
Q-score: 0.521
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ Pubmed: 34526721 DOI: doi:10.1038/s41586-021-03906-4 ]
- Rna polymerase ii elongation complex with csb, csa-ddb1 and uvssa. (Complex)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)
- Csb element (2 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Ts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Nts (14 kDa, DNA from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna repair proteins, csb element and scaffold protein (Complex from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Nts, ts & rna (Complex from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna directed rna polymerase (Complex from Sus scrofa)
- Rna (3 kDa, RNA from Homo sapiens)
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)