Cryo-EM structure of Cas12j19,crRNA and target DNA complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8xca
Q-score: 0.492
To Be Published
- Casj19 (105 kDa, Protein from unidentified)
- Dna (5'-d(p*ap*cp*gp*ap*tp*ap*tp*g)-3') (13 kDa, DNA from unclassified sequences)
- Crrna (19 kDa, RNA from unclassified sequences)
- Ts-dna (13 kDa, DNA from unclassified sequences)
- Ternary complex of cas12j19, crrna and target dna complex (Complex from unidentified)
Cryo-EM structure of Cas12j19 (E100K), crRNA and target DNA complex
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8xcc
Q-score: 0.503
To Be Published
- Nts-dna (13 kDa, DNA from unclassified sequences)
- Crrna (19 kDa, RNA from unclassified sequences)
- Ternary complex of cas12j19(e100k), crrna and target dna complex (Complex from unclassified sequences)
- Ts-dna (13 kDa, DNA from unclassified sequences)
- Cas12j19(e100k) (105 kDa, Protein from unclassified sequences)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9er2
Q-score: 0.448
van den Heuvel D, Rodriguez-Martinez M, van der Meer PJ, Nieto Moreno N, Park J, Kim HS, van Schie JJM, Wondergem AP, D'Souza A, Yakoub G, Herlihy AE, Kashyap K, Boissiere T, Walker J, Mitter R, Apelt K, de Lint K, Kirdok I, Ljungman M, Wolthuis RMF, Cramer P, Scharer OD, Kokic G, Svejstrup JQ, Luijsterburg MS
Cell (2024) 187 pp. 7107- [ DOI: doi:10.1016/j.cell.2024.10.018 Pubmed: 39547229 ]
- Pol ii-tcr-stk19 (Complex from Homo sapiens)
- Rna (5'-r(p*cp*ap*ap*ap*ap*up*cp*gp*ap*gp*ap*gp*gp*a)-3') (4 kDa, RNA from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 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)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa)
- Transcription elongation factor 1 homolog (7 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)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit (19 kDa, Protein from Sus scrofa)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb11-a (13 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Ts (15 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase subunit (218 kDa, Protein from Sus scrofa)
- Isoform 1 of inactive serine/threonine-protein kinase 19 (28 kDa, Protein from Homo sapiens)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- 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)
- Nts (16 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Sus scrofa)
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)
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state I)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s35
Q-score: 0.381
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 ]
- Ts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
- Double-stranded dna (Complex from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA from Klebsiella pneumoniae)
- Dead/deah box helicase (70 kDa, Protein from Klebsiella pneumoniae)
- Type iv-a3 crispr-cas effector complex with ding from klebsiella pneumoniae bound to crrna and target dna (428 kDa, Complex)
- Nts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Crispr effector in complex with a ding helicase and crrna (Complex from Klebsiella pneumoniae)
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein from Klebsiella pneumoniae)
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state II)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s36
Q-score: 0.388
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 ]
- Ts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
- Double-stranded dna (Complex from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA from Klebsiella pneumoniae)
- Dead/deah box helicase (70 kDa, Protein from Klebsiella pneumoniae)
- Crispr effector in complex with a ding helicase and crrna (Complex from Klebsiella pneumoniae)
- Zinc ion (65 Da, Ligand)
- Type iv-a3 crispr-cas effector complex with ding from klebsiella pneumoniae bound to crrna and target dna (Complex)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein from Klebsiella pneumoniae)
- Nts-nda (18 kDa, DNA from Klebsiella pneumoniae)
DNA-bound Type IV-A3 CRISPR effector in complex with DinG helicase from K. pneumoniae (state III)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8s37
Q-score: 0.371
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 ]
- Zinc ion (65 Da, Ligand)
- Crispr type aferr-associated protein csf2 (38 kDa, Protein from Klebsiella pneumoniae)
- Type iv-a3 crispr-cas effector complex with ding from klebsiella pneumoniae bound to crrna and target dna (Complex)
- Dead/deah box helicase (70 kDa, Protein from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf3 (25 kDa, Protein from Klebsiella pneumoniae)
- Ts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Nts-dna (18 kDa, DNA from Klebsiella pneumoniae)
- Crrna (19 kDa, RNA from Klebsiella pneumoniae)
- Double-stranded dna (Complex from Klebsiella pneumoniae)
- Crispr effector in complex with a ding helicase and crrna (Complex from Klebsiella pneumoniae)
- Crispr type aferr-associated protein csf1 (29 kDa, Protein from Klebsiella pneumoniae)
Herbine K, Nayak AR, Temiakov D
Nat Commun (2024) 15 pp. 7134-7134 [ DOI: doi:10.1038/s41467-024-50817-9 Pubmed: 39164235 ]
- Non-template strand dna (nt27mt) (10 kDa, DNA from synthetic construct)
- Template strand dna (ts31mt) (10 kDa, DNA from synthetic construct)
- Rna (rna14mt) (4 kDa, RNA from synthetic construct)
- Diphosphomethylphosphonic acid adenosyl ester (505 Da, Ligand)
- Dna-directed rna polymerase, mitochondrial (127 kDa, Protein from Homo sapiens)
- Transcription elongation factor, mitochondrial (27 kDa, Protein from Homo sapiens)
- Cognate substrate bound in the entry site (es) of human mitochondrial transcription elongation complex (227 kDa, Complex from Homo sapiens)