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)
Bovine adult muscle nAChR resting state
Resolution: 2.09 Å
EM Method: Single-particle
Fitted PDBs: 9avv
Q-score: 0.658
Nature (2024) 632 pp. 1174-1180 [ Pubmed: 39085615 DOI: doi:10.1038/s41586-024-07774-6 ]
- Toxin (6 kDa, Protein from synthetic construct)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bovine muscle nicotinic acetylcholine receptor (Complex from Bos taurus)
- Acetylcholine receptor subunit alpha (49 kDa, Protein from Bos taurus)
- Acetylcholine receptor subunit beta (55 kDa, Protein from Bos taurus)
- Acetylcholine receptor subunit epsilon (52 kDa, Protein from Bos taurus)
- Acetylcholine receptor subunit delta (56 kDa, Protein from Bos taurus)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Bovine fetal muscle nAChR resting state
Resolution: 2.14 Å
EM Method: Single-particle
Fitted PDBs: 9awk
Q-score: 0.634
Nature (2024) 632 pp. 1174-1180 [ Pubmed: 39085615 DOI: doi:10.1038/s41586-024-07774-6 ]
- Toxin (6 kDa, Protein from synthetic construct)
- Acetylcholine receptor subunit gamma (55 kDa, Protein from Bos taurus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Bovine muscle nicotinic acetylcholine receptor (Complex from Bos taurus)
- Acetylcholine receptor subunit alpha (49 kDa, Protein from Bos taurus)
- Acetylcholine receptor subunit beta (55 kDa, Protein from Bos taurus)
- Acetylcholine receptor subunit delta (56 kDa, Protein from Bos taurus)
- (2s)-3-(hexadecanoyloxy)-2-[(9z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate (760 Da, Ligand)
Cryo-EM structure of human gamma-secretase in complex with Abeta43
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 ]
- Dna (Complex)
- Cryoem structure of acecas9 (cleavage intermediate 1) (Complex)
- 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)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein 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 synthetic construct)
- 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)
- Water (18 Da, Ligand)
- 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 (Complex)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- 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)
- Dna target strand (25-mer) (7 kDa, DNA from synthetic construct)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein from Acidothermus cellulolyticus 11B)
- Cryoem structure of acecas9 (pre-cleavage) (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 ]
- Dna (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)
- Water (18 Da, Ligand)
- Cryoem structure of acecas9 (post-cleavage 2) (Complex)
- Single guide rna (106-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein 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 synthetic construct)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*g)-3') (3 kDa, DNA from synthetic construct)
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 ]
- Single guide rna (102-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Dna (Complex)
- Cryoem structure of acecas9 (target bound) (Complex)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein 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)
- Water (18 Da, Ligand)
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 ]
- Dna (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)
- Water (18 Da, Ligand)
- Single guide rna (86-mer) (34 kDa, RNA from Acidothermus cellulolyticus 11B)
- Cryoem structure of acecas9 (post-cleavage 1) (Complex)
- Crispr-associated endonuclease, csn1 family/rna (Complex from Acidothermus cellulolyticus 11B)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated endonuclease, csn1 family (127 kDa, Protein 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 synthetic construct)
- Dna target strand (5'-d(p*cp*cp*ap*gp*gp*ap*tp*cp*tp*tp*g)-3') (3 kDa, DNA from synthetic construct)
Rpd3S in complex with 187bp nucleosome
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8kd2
Q-score: 0.35
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ Pubmed: 37666978 DOI: doi:10.1038/s41422-023-00869-1 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Dna (Complex from synthetic construct)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Linker tightening state of rpd3s-ncp(187bp) (Complex)