Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8w2z
Q-score: 0.415
Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor DW
Nat Commun (2025) 16 pp. 457-457 [ Pubmed: 39774105 DOI: doi:10.1038/s41467-024-55573-4 ]
- Sgrna (50 kDa, RNA from Deltaproteobacteria)
- Hnh nuclease domain-containing protein (86 kDa, Protein from Deltaproteobacteria)
- Cas9d:sgrna:dna (Complex from Deltaproteobacteria)
- Dna non-target strand (4 kDa, DNA from Escherichia phage Lambda)
- Dna target strand (16 kDa, DNA from Escherichia phage Lambda)
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 9auf
Q-score: 0.594
Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor DW
Nat Commun (2025) 16 pp. 457-457 [ Pubmed: 39774105 DOI: doi:10.1038/s41467-024-55573-4 ]
- Sgrna (50 kDa, RNA from Deltaproteobacteria)
- 3' target strand (10 kDa, DNA from Deltaproteobacteria)
- 5' target strand (6 kDa, DNA from Deltaproteobacteria)
- Cas9d ternary complex with a 20bp r-loop (171 kDa, Complex from Deltaproteobacteria)
- Hnh nuclease domain-containing protein (86 kDa, Protein from Deltaproteobacteria)
- Non-target strand (17 kDa, DNA from Deltaproteobacteria)
Cas9 ternary complex, 14-nt sgRNA, State I (linear)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9c9p
Q-score: 0.461
Kiernan KA, Kwon J, Merrill BJ, Simonovic M
Nucleic Acids Res (2025) 53 [ Pubmed: 39657754 DOI: doi:10.1093/nar/gkae1164 ]
- Sgrna (30 kDa, RNA from synthetic construct)
- Non-target strand (12 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Cas9-sgrna-dsdna complex (213 MDa, Complex from Streptococcus pyogenes)
- Target strand (12 kDa, DNA from synthetic construct)
Cas9 ternary complex, 14-nt sgRNA, State II (kinked)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9cgu
Q-score: 0.404
Kiernan KA, Kwon J, Merrill BJ, Simonovic M
Nucleic Acids Res (2025) 53 [ Pubmed: 39657754 DOI: doi:10.1093/nar/gkae1164 ]
- Sgrna (30 kDa, RNA from synthetic construct)
- Non-target strand (12 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Cas9-sgrna-dsdna complex (213 kDa, Complex from Streptococcus pyogenes)
- Target strand (12 kDa, DNA from synthetic construct)
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 [ Pubmed: 39468082 DOI: doi:10.1038/s41467-024-53778-1 ]
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein 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)
- Target strand (ts)-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Non-target strand (nts)-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA 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 [ Pubmed: 39468082 DOI: doi:10.1038/s41467-024-53778-1 ]
- Crispr type aferr-associated protein csf5 (25 kDa, Protein from Pseudomonas oleovorans)
- Target dna (Complex from Pseudomonas oleovorans)
- Crrna (19 kDa, RNA from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf2 (37 kDa, Protein from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf1 (27 kDa, Protein 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 (Complex from Pseudomonas oleovorans)
- Non-target strand (nts) dna (18 kDa, DNA from Pseudomonas oleovorans)
- Zinc ion (65 Da, Ligand)
- Target strand (ts) dna (18 kDa, DNA from Pseudomonas oleovorans)
- Type iv-a1 crispr-cas effector complex from pseudomonas oleovorans bound to crrna and target dna (332 kDa, Complex)
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 [ Pubmed: 39468082 DOI: doi:10.1038/s41467-024-53778-1 ]
- 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 csf5 (25 kDa, Protein from Pseudomonas oleovorans)
- Target dna (Complex from Pseudomonas oleovorans)
- Crrna (19 kDa, RNA from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf2 (37 kDa, Protein from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf1 (27 kDa, Protein from Pseudomonas oleovorans)
- Crispr type aferr-associated protein csf3 (24 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)
- Zinc ion (65 Da, Ligand)
- Non-target strand (nts-) dna (18 kDa, DNA from Pseudomonas oleovorans)
- Atp-dependent dna helicase ding (77 kDa, Protein from Pseudomonas oleovorans)
- Target strand (ts-)dna (18 kDa, DNA from Pseudomonas oleovorans)
Parasitella parasitica Fanzor (PpFz) State 1
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 9cf0
Q-score: 0.412
Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F
Cell (2024) 187 pp. 5238-5252.e20 [ Pubmed: 39208796 DOI: doi:10.1016/j.cell.2024.07.050 ]
- Peptidyl-prolyl cis-trans isomerase (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna non-target strand (17 kDa, DNA from synthetic construct)
- Maltose/maltodextrin-binding periplasmic protein,parasitella parasitica fanzor 1 (144 kDa, Protein from Parasitella parasitica)
- Ternary complex of ppfz1-omegarna-dna (Complex from Parasitella parasitica)
- Dna target strand (17 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Parasitella parasitica fanzor 1 omegarna (19 kDa, RNA from Parasitella parasitica)
Parasitella parasitica Fanzor (PpFz) State 2
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 9cf1
Q-score: 0.365
Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F
Cell (2024) 187 pp. 5238-5252.e20 [ Pubmed: 39208796 DOI: doi:10.1016/j.cell.2024.07.050 ]
- Peptidyl-prolyl cis-trans isomerase (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna non-target strand (17 kDa, DNA from synthetic construct)
- Maltose/maltodextrin-binding periplasmic protein,parasitella parasitica fanzor 1 (144 kDa, Protein from Parasitella parasitica)
- Ternary complex of ppfz1-omegarna-dna (Complex from Parasitella parasitica)
- Dna target strand (17 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Parasitella parasitica fanzor 1 omegarna (19 kDa, RNA from Parasitella parasitica)
Parasitella parasitica Fanzor (PpFz) State 3
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 9cf2
Q-score: 0.399
Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F
Cell (2024) 187 pp. 5238-5252.e20 [ Pubmed: 39208796 DOI: doi:10.1016/j.cell.2024.07.050 ]
- Magnesium ion (24 Da, Ligand)
- Peptidyl-prolyl cis-trans isomerase (17 kDa, Protein from Saccharomyces cerevisiae)
- Dna non-target strand (17 kDa, DNA from synthetic construct)
- Maltose/maltodextrin-binding periplasmic protein,parasitella parasitica fanzor 1 (144 kDa, Protein from Parasitella parasitica)
- Ternary complex of ppfz1-omegarna-dna (Complex from Parasitella parasitica)
- Dna target strand (17 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Parasitella parasitica fanzor 1 omegarna (19 kDa, RNA from Parasitella parasitica)
- Dna substrate model (3 kDa, DNA from synthetic construct)
- Dna substrate model (3 kDa, DNA from synthetic construct)