SpCas9-MMLV RT-pegRNA-target DNA complex (termination)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wus
Q-score: 0.454
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (40-mer) (12 kDa, DNA from Streptococcus pyogenes)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (initiation)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8wut
Q-score: 0.364
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna/rna (35-mer) (10 kDa, Macromolecule from Streptococcus pyogenes)
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
SpCas9-pegRNA-target DNA complex (pre-initiation)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8wuu
Q-score: 0.392
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Spcas9-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
- Dna (34-mer) (10 kDa, DNA from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8wuv
Q-score: 0.354
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Dna (5'-d(*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Dna (50-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 28-nt)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8ygj
Q-score: 0.354
Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O
Nature (2024) 631 pp. 224-231 [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Dna (5'-d(p*tp*gp*ap*tp*gp*gp*cp*ap*gp*ap*gp*tp*ap*cp*tp*ap*g)-3') (5 kDa, DNA from Streptococcus pyogenes)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (62-mer) (19 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
Cryo-EM structure of the AsCas12f-sgRNA-target DNA ternary complex
Resolution: 3.08 Å
EM Method: Single-particle
Fitted PDBs: 8j12
Q-score: 0.479
Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O
Cell (2023) 186 pp. 4920-4935.e23 [ DOI: doi:10.1016/j.cell.2023.08.031 Pubmed: 37776859 ]
- Zinc ion (65 Da, Ligand)
- Rna (247-mer) (72 kDa, RNA from Acidibacillus sulfooxidans)
- Dna (38-mer) (11 kDa, DNA from Acidibacillus sulfooxidans)
- Dna (38-mer) (11 kDa, DNA from Acidibacillus sulfooxidans)
- Ascas12f-sgrna-target dna (Complex from Mycolicibacterium mucogenicum)
- Magnesium ion (24 Da, Ligand)
- Transposase is605 orfb c-terminal domain-containing protein (49 kDa, Protein from Acidibacillus sulfuroxidans)
Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8j1j
Q-score: 0.511
Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O
Cell (2023) 186 pp. 4920-4935.e23 [ DOI: doi:10.1016/j.cell.2023.08.031 Pubmed: 37776859 ]
- Zinc ion (65 Da, Ligand)
- Dna (38-mer) (11 kDa, DNA from Sulfoacidibacillus thermotolerans)
- Ascas12f-yham-sgrnas3-5v7-target dna (Complex from Sulfoacidibacillus thermotolerans)
- Rna (118-mer) (38 kDa, RNA from Sulfoacidibacillus thermotolerans)
- Magnesium ion (24 Da, Ligand)
- Dna (38-mer) (11 kDa, DNA from Sulfoacidibacillus thermotolerans)
- Transposase is605 orfb c-terminal domain-containing protein (49 kDa, Protein from Sulfoacidibacillus thermotolerans)
Cryo-EM structure of the AsCas12f-HKRA-sgRNAS3-5v7-target DNA
Resolution: 2.95 Å
EM Method: Single-particle
Fitted PDBs: 8j3r
Q-score: 0.174
Hino T, Omura SN, Nakagawa R, Togashi T, Takeda SN, Hiramoto T, Tasaka S, Hirano H, Tokuyama T, Uosaki H, Ishiguro S, Kagieva M, Yamano H, Ozaki Y, Motooka D, Mori H, Kirita Y, Kise Y, Itoh Y, Matoba S, Aburatani H, Yachie N, Karvelis T, Siksnys V, Ohmori T, Hoshino A, Nureki O
Cell (2023) 186 pp. 4920-4935.e23 [ DOI: doi:10.1016/j.cell.2023.08.031 Pubmed: 37776859 ]
- Rna (Complex)
- Dna (37-mer) (11 kDa, DNA from Sulfoacidibacillus thermotolerans)
- Zinc ion (65 Da, Ligand)
- Rna (118-mer) (38 kDa, RNA from Sulfoacidibacillus thermotolerans)
- Ascas12f-hkra-sgrnas3-5v7-target dna (Complex from Sulfoacidibacillus thermotolerans)
- Dna (Complex from Sulfoacidibacillus thermotolerans)
- Transposase is605 orfb c-terminal domain-containing protein (49 kDa, Protein from Sulfoacidibacillus thermotolerans)
- Dna (38-mer) (11 kDa, DNA from Sulfoacidibacillus thermotolerans)
- Magnesium ion (24 Da, Ligand)
- Ascas12f-hkra (Complex from Sulfoacidibacillus thermotolerans)
Cryo-EM structure of the TnpB-omegaRNA-target DNA ternary complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8h1j
Q-score: 0.453
Nakagawa R, Hirano H, Omura SN, Nety S, Kannan S, Altae-Tran H, Yao X, Sakaguchi Y, Ohira T, Wu WY, Nakayama H, Shuto Y, Tanaka T, Sano FK, Kusakizako T, Kise Y, Itoh Y, Dohmae N, van der Oost J, Suzuki T, Zhang F, Nureki O
Nature (2023) 616 pp. 390-397 [ DOI: doi:10.1038/s41586-023-05933-9 Pubmed: 37020030 ]
- Rna-guided dna endonuclease tnpb (46 kDa, Protein from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Zinc ion (65 Da, Ligand)
- Non-target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Tnpb-omegarna-target dna ternary complex (Complex from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Omegarna (130-mer) (79 kDa, RNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
- Target strand (10 kDa, DNA from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)
Cryo-EM structure of the Cas12m2-crRNA-target DNA full R-loop complex
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8hhl
Q-score: 0.547
Omura SN, Nakagawa R, Sudfeld C, Villegas Warren R, Wu WY, Hirano H, Laffeber C, Kusakizako T, Kise Y, Lebbink JHG, Itoh Y, van der Oost J, Nureki O
Nat Struct Mol Biol (2023) 30 pp. 1172-1182 [ DOI: doi:10.1038/s41594-023-01042-3 Pubmed: 37460897 ]
- Crrna-target dna (Complex)
- Zinc ion (65 Da, Ligand)
- Ts (36-mer) (10 kDa, DNA from Mycolicibacterium mucogenicum)
- Crrna (Complex)
- Cas12m2 (Complex)
- Cas12m2-crrna-target dna (Complex from Mycolicibacterium mucogenicum)
- Crrna (56-mer) (18 kDa, RNA from Mycolicibacterium mucogenicum)
- Nts (36-mer) (11 kDa, DNA from Mycolicibacterium mucogenicum)
- Target dna (Complex)
- Magnesium ion (24 Da, Ligand)
- Cas12m2 (66 kDa, Protein from Mycolicibacterium mucogenicum)