Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8wt6
Q-score: 0.604
Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H
Nature (2024) 630 pp. 994-1002 [ Pubmed: 38926616 DOI: doi:10.1038/s41586-024-07570-2 ]
- Donor dna (13 kDa, DNA from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- The is621 recombinase in complex with bridge rna, donor dna, and target dna in the pre-strand exchange state (Complex from Escherichia coli)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Is621 transposase (36 kDa, Protein from Escherichia coli)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8wt7
Q-score: 0.563
Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H
Nature (2024) 630 pp. 994-1002 [ Pubmed: 38926616 DOI: doi:10.1038/s41586-024-07570-2 ]
- Donor dna (13 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Target dna (11 kDa, DNA from Escherichia coli)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- The is621 recombinase in complex with bridge rna, donor dna, and target dna in the pre-strand exchange locked state (Complex from Escherichia coli)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Is621 transposase (36 kDa, Protein from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wt8
Q-score: 0.543
Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H
Nature (2024) 630 pp. 994-1002 [ Pubmed: 38926616 DOI: doi:10.1038/s41586-024-07570-2 ]
- Donor dna-target dna (10 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Is621 transposase (36 kDa, Protein from Escherichia coli)
- The is621 recombinase in complex with bridge rna, donor dna, and target dna in the post-strand exchange state (holliday junction intermediate) (Complex from Escherichia coli)
- Target dna-donor dna (15 kDa, DNA from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8wt9
Q-score: 0.57
Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H
Nature (2024) 630 pp. 994-1002 [ Pubmed: 38926616 DOI: doi:10.1038/s41586-024-07570-2 ]
- The is621 recombinase in complex with bridge rna, donor dna, and target dna in the post-strand exchange state (holliday junction resolution) (Complex from Escherichia coli)
- Donor dna-target dna (10 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Is621 transposase (36 kDa, Protein from Escherichia coli)
- Target dna-donor dna (15 kDa, DNA from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease
Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, Nishimasu H
Science (2022) 378 pp. 882-889 [ DOI: 10.1126/science.add7347 Pubmed: 36423304 ]
Image sets:
Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex
Kato K, Zhou W, Okazaki S, Isayama Y, Nishizawa T, Gootenberg JS, Abudayyeh OO, Nishimasu H
Cell (2022) 185 pp. 2324-2337.e16 [ DOI: 10.1016/j.cell.2022.05.003 Pubmed: 35643083 ]
Image sets:
Structure of the OgeuIscB-omega RNA-target DNA complex
Resolution: 2.55 Å
EM Method: Single-particle
Fitted PDBs: 7xht
Q-score: 0.619
Kato K, Okazaki S, Kannan S, Altae-Tran H, Esra Demircioglu F, Isayama Y, Ishikawa J, Fukuda M, Macrae RK, Nishizawa T, Makarova KS, Koonin EV, Zhang F, Nishimasu H
Nat Commun (2022) 13 pp. 6719-6719 [ Pubmed: 36344504 DOI: doi:10.1038/s41467-022-34378-3 ]
- Dna (5'-d(p*gp*ap*ap*gp*ap*ap*ap*ap*cp*cp*ap*t)-3') (4 kDa, DNA from synthetic construct)
- Ogeuiscb (56 kDa, Protein from metagenome)
- Magnesium ion (24 Da, Ligand)
- Structure of the iscb-omegarna ribonucleoprotein complex (Complex)
- Iscb-omegarna (Complex from metagenome)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Dna (Complex)
- Rna (228-mer) (73 kDa, RNA from metagenome)
- Dna (49-mer) (15 kDa, DNA from synthetic construct)
Structure of the Cas7-11-Csx29-guide RNA complex
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 7y9x
Q-score: 0.59
Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, Nishimasu H
Science (2022) 378 pp. 882-889 [ DOI: doi:10.1126/science.add7347 Pubmed: 36423304 ]
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Zinc ion (65 Da, Ligand)
- Cas7-11, csx29 (Complex from Desulfonema ishimotonii)
- Crrna (12 kDa, RNA from Desulfonema ishimotonii)
- Rna (Complex)
Structure of the Cas7-11-Csx29-guide RNA-target RNA (no PFS) complex
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 7y9y
Q-score: 0.564
Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, Nishimasu H
Science (2022) 378 pp. 882-889 [ DOI: doi:10.1126/science.add7347 Pubmed: 36423304 ]
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Cas7-11, csx29 (Complex)
- Zinc ion (65 Da, Ligand)
- Rna (27-mer) (8 kDa, RNA from Desulfonema ishimotonii)
- Crrna, target rna (Complex from Desulfonema ishimotonii)
- Rna (38-mer) (12 kDa, RNA from Desulfonema ishimotonii)
Structure of the Cas7-11-Csx29-guide RNA-target RNA (non-matching PFS) complex
Resolution: 2.84 Å
EM Method: Single-particle
Fitted PDBs: 8gs2
Q-score: 0.571
Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, Nishimasu H
Science (2022) 378 pp. 882-889 [ DOI: doi:10.1126/science.add7347 Pubmed: 36423304 ]
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Crrna (Complex)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Cytidine-5'-monophosphate (323 Da, Ligand)
- Adenosine monophosphate (347 Da, Ligand)
- Crrna (30 kDa, RNA from Desulfonema ishimotonii)
- Cas7-11, csx29 (Complex)
- Zinc ion (65 Da, Ligand)
- Target rna with non-matching pfs (10 kDa, RNA from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Target rna with 3'-tag (Complex from Desulfonema ishimotonii)