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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) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- 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)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna (40-mer) (12 kDa, DNA 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) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- 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)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 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)
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) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Rna (137-mer) (44 kDa, RNA 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)
- Dna (51-mer) (15 kDa, DNA 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) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Rna (137-mer) (44 kDa, RNA 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)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- 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) [ DOI: doi:10.1038/s41586-024-07497-8 Pubmed: 38811740 ]
- Rna (137-mer) (44 kDa, RNA from Streptococcus pyogenes)
- Dna (62-mer) (19 kDa, DNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- 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)
SpRY-Cas9:gRNA complex bound to non-target DNA with 10 bp R-loop
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8t79
Q-score: 0.383
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ Pubmed: 38688943 DOI: doi:10.1038/s41467-024-47830-3 ]
- Ts (6 kDa, DNA from Escherichia phage Lambda)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Grna (28 kDa, RNA from Streptococcus pyogenes)
- Nts (2 kDa, DNA from Escherichia phage Lambda)
- Ternary complex of spry-cas9 with grna and non-target dna with 10 bp r-loop (211 kDa, Complex from Streptococcus pyogenes)
SpRY-Cas9:gRNA complex targeting TGG PAM DNA
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8spq
Q-score: 0.431
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ Pubmed: 38688943 DOI: doi:10.1038/s41467-024-47830-3 ]
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes serotype M1)
- Ts (16 kDa, DNA from Escherichia phage Lambda)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Ternary complex of spry-cas9 with lambda 1 grna and lambda 1 dna (211 kDa, Complex from Streptococcus pyogenes)
- Nts (5 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Ts (5 kDa, DNA from Escherichia phage Lambda)
SpRY-Cas9:gRNA complex targeting TTC PAM DNA
Resolution: 3.69 Å
EM Method: Single-particle
Fitted PDBs: 8sqh
Q-score: 0.379
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ Pubmed: 38688943 DOI: doi:10.1038/s41467-024-47830-3 ]
- Ts (4 kDa, DNA from Escherichia phage Lambda)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Ternary complex of spry-cas9 with lambda 1 grna and lambda 1 dna oligo (211 kDa, Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Ts (5 kDa, DNA from Escherichia phage Lambda)
SpRY-Cas9:gRNA complex targeting TAC PAM DNA
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8srs
Q-score: 0.521
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ Pubmed: 38688943 DOI: doi:10.1038/s41467-024-47830-3 ]
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Ternary complex of spry-cas9 with lambda 1 grna and lambda 1 dna (211 kDa, Complex from Streptococcus pyogenes)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Water (18 Da, Ligand)
- Ts (3 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Ts (5 kDa, DNA from Escherichia phage Lambda)
SpRY-Cas9:gRNA complex targeting TAC PAM DNA with 0 bp R-loop
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8t6o
Q-score: 0.387
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ Pubmed: 38688943 DOI: doi:10.1038/s41467-024-47830-3 ]
- Ternary complex of spry-cas9 with grna and nac pam dna after one minute of dna incubation with 0 bp r-loop (211 kDa, Complex from Streptococcus pyogenes)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Grna (27 kDa, RNA from Streptococcus pyogenes)
- Ts (16 kDa, DNA from Escherichia phage Lambda)