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 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 (49-mer) (15 kDa, DNA from synthetic construct)
- Structure of the iscb-omegarna ribonucleoprotein complex (Complex)
- Ogeuiscb (56 kDa, Protein from metagenome)
- Rna (228-mer) (73 kDa, RNA from metagenome)
- Magnesium ion (24 Da, Ligand)
- Dna (5'-d(p*gp*ap*ap*gp*ap*ap*ap*ap*cp*cp*ap*t)-3') (4 kDa, DNA from synthetic construct)
- Dna (Complex)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Iscb-omegarna (Complex from metagenome)
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 [ Pubmed: 36423304 DOI: doi:10.1126/science.add7347 ]
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Crrna (12 kDa, RNA from Desulfonema ishimotonii)
- Cas7-11, csx29 (Complex from Desulfonema ishimotonii)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Zinc ion (65 Da, Ligand)
- Cas7-11 in complex with a crrna and its target rna (Complex 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 [ Pubmed: 36423304 DOI: doi:10.1126/science.add7347 ]
- Crrna, target rna (Complex from Desulfonema ishimotonii)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Zinc ion (65 Da, Ligand)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Cas7-11, csx29 (Complex)
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Rna (38-mer) (12 kDa, RNA from Desulfonema ishimotonii)
- Rna (27-mer) (8 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 [ Pubmed: 36423304 DOI: doi:10.1126/science.add7347 ]
- Adenosine monophosphate (347 Da, Ligand)
- Crrna (30 kDa, RNA from Desulfonema ishimotonii)
- Crispr-associated ramp family protein (185 kDa, Protein from Desulfonema ishimotonii)
- Chat domain-containing protein (88 kDa, Protein from Desulfonema ishimotonii)
- Crrna (Complex)
- Cas7-11 in complex with a crrna and its target rna (Complex from Desulfonema ishimotonii)
- Target rna with 3'-tag (Complex from Desulfonema ishimotonii)
- Cytidine-5'-monophosphate (323 Da, Ligand)
- Cas7-11, csx29 (Complex)
- Zinc ion (65 Da, Ligand)
- Target rna with non-matching pfs (10 kDa, RNA from Desulfonema ishimotonii)
Structure of IsrB ternary complex with RNA mutant and target DNA
Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F
Nature (2022) 610 pp. 575-581 [ DOI: doi:10.1038/s41586-022-05324-6 Pubmed: 36224386 ]
Structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with omega RNA and target DNA
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8dmb
Q-score: 0.523
Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F
Nature (2022) 610 pp. 575-581 [ DOI: doi:10.1038/s41586-022-05324-6 Pubmed: 36224386 ]
- Omega rna (91 kDa, RNA from Desulfovirgula thermocuniculi)
- Dtisrb-wrna-tgdna complex (Complex)
- Ubiquitin-like protein smt3,isrb protein,monomeric superfolder green fluorescent protein (84 kDa, Protein from synthetic construct)
- Target dna (9 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Non-target dna (3 kDa, DNA from synthetic construct)
Avs3 bound to phage PhiV-1 terminase, C2 refinement of Cap4 nuclease domain
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8dgc
Q-score: 0.218
Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F
Science (2022) 377 pp. eabm4096-eabm4096 [ Pubmed: 35951700 DOI: doi:10.1126/science.abm4096 ]
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Terminase, large subunit (66 kDa, Protein from Escherichia phage PhiV-1)
- Magnesium ion (24 Da, Ligand)
- Seavs3 (236 kDa, Protein from Salmonella enterica)
- Avs3 bound to phage phiv-1 terminase (1 MDa, Complex)
Avs4 bound to phage PhiV-1 portal, C2 refinement of Mrr nuclease domain
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8dgf
Q-score: 0.234
Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F
Science (2022) 377 pp. eabm4096-eabm4096 [ DOI: doi:10.1126/science.abm4096 Pubmed: 35951700 ]
- Atp-binding protein avs4 (186 kDa, Protein from Escherichia coli)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Avs4 bound to phage phiv-1 portal (980 kDa, Complex)
- Magnesium ion (24 Da, Ligand)
- Portal protein (58 kDa, Protein from Escherichia phage PhiV-1)
Avs3 bound to PhiV-1 terminase, symmetry-expanded C1 refinement of TPR-terminase domain
Gao LA, Wilkinson ME, Strecker J, Makarova KS, Macrae RK, Koonin EV, Zhang F
Science (2022) 377 pp. eabm4096-eabm4096 [ DOI: doi:10.1126/science.abm4096 Pubmed: 35951700 ]