CryoEM structure of ThermoCas9 in post-cleavage state bound with the DNA containing NNNNCCA PAM
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 9ar4
Q-score: 0.558
Roth M, Shu Y, Trasanidis D, Zhao Y, Hoffman R, van der Oost J, Li H
To Be Published
- Single guide rna (47 kDa, RNA from Geobacillus thermodenitrificans)
- Cleaved 5' target dna strand (4 kDa, DNA from synthetic construct)
- Cleaved 5' non-target dna strand (1 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Thermocas9 post-cleavage complex (Complex from Geobacillus thermodenitrificans)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cleaved 3' target dna strand (7 kDa, DNA from synthetic construct)
- Cleaved 3' non-target dna strand (4 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas9 (126 kDa, Protein from Geobacillus thermodenitrificans)
Structure of Acidothermus cellulolyticus Cas9 bound with methylated DNA
Resolution: 2.88 Å
EM Method: Single-particle
Fitted PDBs: 9ar5
Q-score: -0.063
Roth MO, Shu Y, Zhao Y, Trasanidou D, Hoffman RD, Trasanidis N, Gelasco MK, Medina ML, Das D, Rai J, Wang B, Li H
To Be Published
- Dna/rna (5'-d(p*tp*ap*cp*a)-r(p*(5mc))-d(p*cp*ap*ap*gp*cp*t)-3') (3 kDa, DNA from Acidothermus cellulolyticus)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus)
- Crispr-cas9 (Complex from Acidothermus cellulolyticus)
- Rna (92-mer) (34 kDa, RNA from Acidothermus cellulolyticus)
- Dna (25-mer) (7 kDa, DNA from Acidothermus cellulolyticus)
CryoEM structure of ThermoCas9 in pre-cleavage state bound with the DNA containing NNNNCCA PAM
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 9ar6
Q-score: 0.501
Roth M, Shu Y, Trasanidou D, Zhao Y, van der Oost J, Li H
To Be Published
- Ternary complex of thermocas9 with single guide rna and target dna (Complex from Geobacillus thermodenitrificans)
- Water (18 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Target-strand dna (12 kDa, DNA from Geobacillus thermodenitrificans)
- Non-target dna (3 kDa, DNA from Geobacillus thermodenitrificans)
- Crispr-associated endonuclease cas9 (126 kDa, Protein from Geobacillus thermodenitrificans)
- Single guide rna (47 kDa, RNA from Geobacillus thermodenitrificans)
CryoEM structure of ThermoCas9 bound with target DNA strand only
Resolution: 2.52 Å
EM Method: Single-particle
Fitted PDBs: 9ar7
Q-score: 0.518
Roth M, Shu Y, Trasandidou D, Zhao Y, van der Oost J, Li H
To Be Published
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Cleaved 5' target strand (4 kDa, DNA from Geobacillus thermodenitrificans)
- Cleaved 3' target dna strand (12 kDa, DNA from Geobacillus thermodenitrificans)
- Single guide rna (47 kDa, RNA from Geobacillus thermodenitrificans)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Ternary complex of thermocas9 with rna and dna (Complex from Geobacillus thermodenitrificans NG80-2)
- Crispr-associated endonuclease cas9 (126 kDa, Protein from Geobacillus thermodenitrificans)
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)
Structure of Acidothermus cellulolyticus Cas9 ternary complex (Post-cleavage 1)
Resolution: 2.58 Å
EM Method: Single-particle
Fitted PDBs: 8d2q
Q-score: 0.522
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 ]
- Single guide rna (86-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- 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 1) (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)
- Dna (Complex)