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)
Resolution: 2.73 Å
EM Method: Single-particle
Fitted PDBs: 9auf
Q-score: 0.594
Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor DW
Nat Commun (2025) 16 pp. 457-457 [ Pubmed: 39774105 DOI: doi:10.1038/s41467-024-55573-4 ]
- Sgrna (50 kDa, RNA from Deltaproteobacteria)
- 3' target strand (10 kDa, DNA from Deltaproteobacteria)
- 5' target strand (6 kDa, DNA from Deltaproteobacteria)
- Cas9d ternary complex with a 20bp r-loop (171 kDa, Complex from Deltaproteobacteria)
- Hnh nuclease domain-containing protein (86 kDa, Protein from Deltaproteobacteria)
- Non-target strand (17 kDa, DNA from Deltaproteobacteria)
Structure of PsCas9 in complex with gRNA and DNA in product state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8umf
Q-score: 0.526
To Be Published
- Magnesium ion (24 Da, Ligand)
- Cas9 (168 kDa, Protein from Parasutterella secunda)
- Rna (121-mer) (41 kDa, RNA from synthetic construct)
- Dna (80-mer) (24 kDa, DNA from synthetic construct)
- Dna (80-mer) (24 kDa, DNA from synthetic construct)
- Pscas9 in with grna and dsdna, product state (211 kDa, Complex from Parasutterella secunda)
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)
Structure of CbCas9 bound to 20-nucleotide complementary DNA substrate
Resolution: 2.46 Å
EM Method: Single-particle
Fitted PDBs: 8iyq
Q-score: 0.513
Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG
Nature (2024) 630 pp. 484-492 [ Pubmed: 38811729 DOI: doi:10.1038/s41586-024-07486-x ]
- Ts (8 kDa, DNA from Chryseobacterium)
- Nts (8 kDa, DNA from Chryseobacterium)
- Sgrna (40 kDa, RNA from Chryseobacterium)
- Deadcbcas9 (170 kDa, Protein from Chryseobacterium)
- Structure of cbcas9 bound to 20-nucleotide complementary dna substrate (228 kDa, Complex from Chryseobacterium)
Structure of CbCas9 bound to 6-nucleotide complementary DNA substrate
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8wmh
Q-score: 0.279
Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG
Nature (2024) 630 pp. 484-492 [ Pubmed: 38811729 DOI: doi:10.1038/s41586-024-07486-x ]
- Ts (8 kDa, DNA from Chryseobacterium)
- Structure of cbcas9 bound to 6-nucleotide complementary dna substrate (228 kDa, Complex from Chryseobacterium)
- Nts (8 kDa, DNA from Chryseobacterium)
- Sgrna (40 kDa, RNA from Chryseobacterium)
- Deadcbcas9 (170 kDa, Protein from Chryseobacterium)
Structure of CbCas9-PcrIIC1 complex bound to 28-bp DNA substrate (20-nt complementary)
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8wmm
Q-score: 0.342
Zhang S, Sun A, Qian JM, Lin S, Xing W, Yang Y, Zhu HZ, Zhou XY, Guo YS, Liu Y, Meng Y, Jin SL, Song W, Li CP, Li Z, Jin S, Wang JH, Dong MQ, Gao C, Chen C, Bai Y, Liu JG
Nature (2024) 630 pp. 484-492 [ Pubmed: 38811729 DOI: doi:10.1038/s41586-024-07486-x ]
- Magnesium ion (24 Da, Ligand)
- Pcriic1 (15 kDa, Protein from Chryseobacterium)
- Ts (8 kDa, DNA from Chryseobacterium)
- Structure of cbcas9-pcriic1 complex bound to 28-bp dna substrate (20-nt complementary) (469 kDa, Complex from Chryseobacterium)
- Nts (8 kDa, DNA from Chryseobacterium)
- Sgrna (40 kDa, RNA from Chryseobacterium)
- Deadcbcas9 (170 kDa, Protein from Chryseobacterium)