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:
Icosahedral capsid of the phicrAss001 virion
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 7qof
Q-score: 0.575
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
- Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
- Head fiber trimer protein gp21 (13 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Head fiber dimer protein gp29 (10 kDa, Protein from Bacteroides phage crAss001)
- Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
- Magnesium ion (24 Da, Ligand)
Portal protein assembly of the phicrAss001 virion with C12 symmetry imposed
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7qog
Q-score: 0.583
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
- Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
Unique vertex of the phicrAss001 virion with C5 symmetry imposed
Resolution: 3.32 Å
EM Method: Single-particle
Fitted PDBs: 7qoh
Q-score: 0.559
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
- Head fiber trimer protein gp21 (10 kDa, Protein from Bacteroides phage crAss001)
- Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
- Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
- Portal vertex capsid protein gp57 (11 kDa, Protein from Bacteroides phage crAss001)
- Magnesium ion (24 Da, Ligand)
Unique vertex of the phicrAss001 virion
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 7qoi
Q-score: 0.505
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
- Head fiber trimer protein gp21 (10 kDa, Protein from Bacteroides phage crAss001)
- Major capsid protein gp32 (57 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
- Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
- Auxiliary capsid protein gp36 (36 kDa, Protein from Bacteroides phage crAss001)
- Portal vertex capsid protein gp57 (11 kDa, Protein from Bacteroides phage crAss001)
- Magnesium ion (24 Da, Ligand)
Tail barrel assembly of the phicrAss001 virion with C12 symmetry imposed
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 7qoj
Q-score: 0.562
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
- Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
- Tail fiber protein gp22 (92 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
- Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Tail hub protein a gp38 (24 kDa, Protein from Bacteroides phage crAss001)
- Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 4/5 gp34 (26 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 3 gp35 (26 kDa, Protein from Bacteroides phage crAss001)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Tail hub protein b gp39 (13 kDa, Protein from Bacteroides phage crAss001)
Tail muzzle assembly of the phicrAss001 virion with C6 symmetry imposed
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7qok
Q-score: 0.529
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Ring protein 4/5 gp34 (26 kDa, Protein from Bacteroides phage crAss001)
- Muzzle bound helix (1 kDa, Protein from Bacteroides phage crAss001)
- Muzzle protein gp44 (156 kDa, Protein from Bacteroides phage crAss001)
- Magnesium ion (24 Da, Ligand)
Tail assembly of the phicrAss001 virion with C6 symmetry imposed
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 7qol
Q-score: 0.525
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
- Ring protein 2 gp40 (26 kDa, Protein from Bacteroides phage crAss001)
- Tail fiber protein gp22 (92 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 1 gp43 (27 kDa, Protein from Bacteroides phage crAss001)
- Cargo protein 1 gp45 (90 kDa, Protein from Bacteroides phage crAss001)
- Bacteroides phage crass001 (Virus from Bacteroides phage crAss001)
- Tail hub protein a gp38 (24 kDa, Protein from Bacteroides phage crAss001)
- Portal protein gp20 (93 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 4/5 gp34 (26 kDa, Protein from Bacteroides phage crAss001)
- Muzzle protein gp44 (156 kDa, Protein from Bacteroides phage crAss001)
- Muzzle bound helix (1 kDa, Protein from Bacteroides phage crAss001)
- Ring protein 3 gp35 (26 kDa, Protein from Bacteroides phage crAss001)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Tail hub protein b gp39 (13 kDa, Protein from Bacteroides phage crAss001)
Asymmetric reconstruction of the phicrAss001 virion
Bayfield OW, Shkoporov AN, Yutin N, Khokhlova EV, Smith JLR, Hawkins DEDP, Koonin EV, Hill C, Antson AA
Nature (2023) 617 pp. 409-416 [ Pubmed: 37138077 DOI: doi:10.1038/s41586-023-06019-2 ]
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 ]
- Ogeuiscb (56 kDa, Protein from metagenome)
- Rna (228-mer) (73 kDa, RNA from metagenome)
- Dna (Complex)
- Iscb-omegarna (Complex 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)
- Lauryl dimethylamine-n-oxide (229 Da, Ligand)
- Magnesium ion (24 Da, Ligand)