Cryo-EM structure of Cas9-sgRNA-A32 complex
Zheng J, Zhu Y, Huang T, Gao W, He J, Huang Z
Sci China Life Sci (2024) 67 pp. 1781-1791 [ Pubmed: 38842649 DOI: doi:10.1007/s11427-024-2607-8 ]
- Cas9-sgrna-a32 complex (Complex from Streptococcus pyogenes)
- A32 (16 kDa, Protein from Streptococcus)
- Rna (92-mer) (29 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
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 ]
- Gag-pol polyprotein (55 kDa, Protein from Moloney murine leukemia virus)
- Dna (51-mer) (15 kDa, DNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes serotype M1)
- Rna (115-mer) (37 kDa, RNA from Streptococcus pyogenes)
- Spcas9-mmlv rt-pegrna-target dna complex (Complex from Streptococcus pyogenes)
- Dna (40-mer) (12 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)
Cryo-EM structure of iGeoCas9 in complex with sgRNA and target DNA
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 8uzb
Q-score: 0.561
Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA
Cell (2024) 187 pp. 3249- [ DOI: doi:10.1016/j.cell.2024.04.031 Pubmed: 38781968 ]
- Non-target strand dna (15 kDa, DNA from Mus musculus)
- Crispr-associated endonuclease cas9 (127 kDa, Protein from Geobacillus stearothermophilus)
- Ternary complex of deactivated igeocas9 with sgrna and target dna (203 kDa, Complex from Geobacillus stearothermophilus)
- Target strand dna (39-mer) (15 kDa, DNA from Mus musculus)
- Rna (107-mer) (44 kDa, RNA from Geobacillus stearothermophilus)
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 [ DOI: doi:10.1038/s41467-024-47830-3 Pubmed: 38688943 ]
- Ts (5 kDa, DNA from Escherichia phage Lambda)
- Magnesium ion (24 Da, Ligand)
- Nts (16 kDa, DNA from Escherichia phage Lambda)
- Water (18 Da, Ligand)
- Ternary complex of spry-cas9 with lambda 1 grna and lambda 1 dna (211 kDa, Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Grna (31 kDa, RNA from Streptococcus pyogenes)
- Ts (3 kDa, DNA from Escherichia phage Lambda)
SpRY-Cas9:gRNA complex bound to non-target DNA with 1 bp R-loop
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 8t6y
Q-score: 0.465
Hibshman GN, Bravo JPK, Hooper MM, Dangerfield TL, Zhang H, Finkelstein IJ, Johnson KA, Taylor DW
Nat Commun (2024) 15 pp. 3663-3663 [ DOI: doi:10.1038/s41467-024-47830-3 Pubmed: 38688943 ]
- Nts (3 kDa, DNA from Escherichia phage Lambda)
- Ternary complex of spry-cas9 with grna and non-target dna with 1 bp r-loop (211 kDa, Complex from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (159 kDa, Protein from Streptococcus pyogenes)
- Ts (3 kDa, DNA from Escherichia phage Lambda)
- Grna (28 kDa, RNA from Streptococcus pyogenes)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Cleavage Intermediate 2)
Resolution: 2.43 Å
EM Method: Single-particle
Fitted PDBs: 8d2k
Q-score: 0.626
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*gp*cp*cp*ap*tp*cp*cp*tp*ap*cp*cp*tp*cp*t)-3') (7 kDa, DNA from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Water (18 Da, Ligand)
- Dna non-target strand (5'-d(p*tp*ap*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from Acidothermus cellulolyticus 11B)
- Cryoem structure of acecas9 (cleavage intermediate 2) (Complex)
- Single guide rna (102-mer) (34 kDa, RNA from Acidothermus cellulolyticus)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Dna non-target strand (5'-d(p*ap*gp*a)-3') (910 Da, DNA from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(*ap*gp*cp*tp*tp*gp*gp*tp*gp*tp*ap*tp*a)-3') (4 kDa, DNA from Acidothermus cellulolyticus 11B)
- Dna (Complex)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Cleavage Intermediate 1)
Resolution: 2.21 Å
EM Method: Single-particle
Fitted PDBs: 8d2l
Q-score: 0.661
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*gp*cp*cp*ap*tp*cp*cp*tp*ap*cp*cp*tp*cp*t)-3') (7 kDa, DNA from synthetic construct)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Cryoem structure of acecas9 (cleavage intermediate 1) (Complex)
- Dna target strand (5'-d(*ap*gp*cp*tp*tp*gp*gp*tp*gp*tp*ap*tp*a)-3') (4 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Dna non-target strand (5'-d(p*tp*ap*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from synthetic construct)
- Dna (Complex)
- Dna non-target strand (5'-d(p*ap*gp*a)-3') (910 Da, DNA from synthetic construct)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Pre-cleavage)
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 8d2n
Q-score: 0.459
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Dna non-target strand (5'-d(p*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Dna target strand (25-mer) (7 kDa, DNA from synthetic construct)
- Cryoem structure of acecas9 (pre-cleavage) (Complex)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Dna (Complex)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Post-cleavage 2)
Resolution: 2.66 Å
EM Method: Single-particle
Fitted PDBs: 8d2o
Q-score: 0.56
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*g)-3') (3 kDa, DNA from synthetic construct)
- Dna target strand (5'-d(*ap*gp*cp*tp*tp*gp*gp*tp*gp*tp*ap*tp*a)-3') (4 kDa, DNA from synthetic construct)
- Cryoem structure of acecas9 (post-cleavage 2) (Complex)
- Dna non-target strand (5'-d(p*ap*tp*ap*cp*ap*cp*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Dna (Complex)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Target bound)
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 8d2p
Q-score: 0.572
Das A, Rai J, Roth MO, Shu Y, Medina ML, Barakat MR, Li H
Nat Catal (2023) 6 pp. 969-977 [ DOI: doi:10.1038/s41929-023-01031-1 Pubmed: 38348449 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*gp*cp*cp*ap*tp*cp*cp*tp*ap*cp*cp*tp*cp*t)-3') (7 kDa, DNA from synthetic construct)
- Single guide rna (102-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Dna (Complex)
- Cryoem structure of acecas9 (target bound) (Complex)