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
- Cleaved 5' target dna strand (4 kDa, DNA from synthetic construct)
- Thermocas9 post-cleavage complex (Complex from Geobacillus thermodenitrificans)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cleaved 5' non-target dna strand (1 kDa, DNA from synthetic construct)
- Cleaved 3' target dna strand (7 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease cas9 (126 kDa, Protein from Geobacillus thermodenitrificans)
- Cleaved 3' non-target dna strand (4 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- Single guide rna (47 kDa, RNA 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 (25-mer) (7 kDa, DNA from Acidothermus cellulolyticus)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus)
- 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)
- Rna (92-mer) (34 kDa, RNA from Acidothermus cellulolyticus)
- Crispr-cas9 (Complex 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
- Target-strand dna (12 kDa, DNA from Geobacillus thermodenitrificans)
- Sodium ion (22 Da, Ligand)
- Ternary complex of thermocas9 with single guide rna and target dna (Complex from Geobacillus thermodenitrificans)
- Non-target dna (3 kDa, DNA from Geobacillus thermodenitrificans)
- Single guide rna (47 kDa, RNA from Geobacillus thermodenitrificans)
- Crispr-associated endonuclease cas9 (126 kDa, Protein from Geobacillus thermodenitrificans)
- Water (18 Da, Ligand)
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
- Cleaved 5' target strand (4 kDa, DNA from Geobacillus thermodenitrificans)
- Water (18 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Cleaved 3' target dna strand (12 kDa, DNA from Geobacillus thermodenitrificans)
- Single guide rna (47 kDa, RNA from Geobacillus thermodenitrificans)
- Crispr-associated endonuclease cas9 (126 kDa, Protein from Geobacillus thermodenitrificans)
- Magnesium ion (24 Da, Ligand)
- Ternary complex of thermocas9 with rna and dna (Complex from Geobacillus thermodenitrificans NG80-2)
Structure of Cas9-sgRNA ribonucleoprotein bound to nucleosome
Resolution: 4.52 Å
EM Method: Single-particle
Fitted PDBs: 8yny
Q-score: 0.218
Nagamura R, Kujirai T, Kato J, Shuto Y, Kusakizako T, Hirano H, Endo M, Toki S, Saika H, Kurumizaka H, Nureki O
Nat Commun (2024) 15 pp. 10744-10744 [ Pubmed: 39737984 DOI: doi:10.1038/s41467-024-54768-z ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (175-mer) (53 kDa, DNA from Homo sapiens)
- Spcas9-sgrna-nucleosome ternary complex (Complex from Homo sapiens)
- Rna (97-mer) (31 kDa, RNA from Streptococcus pyogenes)
- Crispr-associated endonuclease cas9/csn1 (158 kDa, Protein from Streptococcus pyogenes)
- Dna (17-mer) (5 kDa, DNA from Homo sapiens)
- Dna (176-mer) (54 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
SpCas9-MMLV RT-pegRNA-target DNA complex (termination) overall map
SpCas9-MMLV RT-pegRNA-target DNA complex (termination) focused map
SpCas9-MMLV RT-pegRNA-target DNA complex (initiation) overall map
SpCas9-MMLV RT-pegRNA-target DNA complex (initiation) focused map
SpCas9-MMLV RT-pegRNA-target DNA complex (elongation 16-nt) overall map