Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA
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: 10.1038/s41586-024-07570-2 ]
Image sets:
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 [ DOI: doi:10.1038/s41586-024-07570-2 Pubmed: 38926616 ]
- Target dna (11 kDa, DNA from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
- 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)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- Water (18 Da, Ligand)
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 [ DOI: doi:10.1038/s41586-024-07570-2 Pubmed: 38926616 ]
- Target dna (11 kDa, DNA 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)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- Water (18 Da, Ligand)
- The is621 recombinase in complex with bridge rna, donor dna, and target dna in the pre-strand exchange locked state (Complex 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 [ DOI: doi:10.1038/s41586-024-07570-2 Pubmed: 38926616 ]
- 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)
- Is621 transposase (36 kDa, Protein from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Target dna-donor dna (15 kDa, DNA from Escherichia coli)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- Donor dna-target dna (10 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 [ DOI: doi:10.1038/s41586-024-07570-2 Pubmed: 38926616 ]
- 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)
- Is621 transposase (36 kDa, Protein from Escherichia coli)
- Target dna (11 kDa, DNA from Escherichia coli)
- Donor dna (13 kDa, DNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Target dna-donor dna (15 kDa, DNA from Escherichia coli)
- Bridge rna (57 kDa, RNA from Escherichia coli)
- Water (18 Da, Ligand)
- Donor dna-target dna (10 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 [ DOI: doi:10.1038/s41467-022-34378-3 Pubmed: 36344504 ]
- Dna (Complex)
- Iscb-omegarna (Complex from metagenome)
- Rna (228-mer) (73 kDa, RNA from metagenome)
- Dna (5'-d(p*gp*ap*ap*gp*ap*ap*ap*ap*cp*cp*ap*t)-3') (4 kDa, DNA from synthetic construct)
- Dna (49-mer) (15 kDa, DNA from synthetic construct)
- Structure of the iscb-omegarna ribonucleoprotein complex (Complex)
- Magnesium ion (24 Da, Ligand)
- Ogeuiscb (56 kDa, Protein from metagenome)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
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 ]
- Rna (Complex)
- Zinc ion (65 Da, Ligand)
- Cas7-11, csx29 (Complex from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Crrna (12 kDa, RNA 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)
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 ]
- Zinc ion (65 Da, Ligand)
- 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)
- Cas7-11, csx29 (Complex)
- Crrna, target rna (Complex from Desulfonema ishimotonii)
- Rna (27-mer) (8 kDa, RNA from Desulfonema ishimotonii)
- Rna (38-mer) (12 kDa, RNA from Desulfonema ishimotonii)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)