Cryo-EM structure of Cas5-HNH Cascade bound with sDNA, Conf2
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8zp9
Q-score: 0.459
Liu YN, Wang L, Zhang H, Zhu H
To Be Published
- Crispr system cascade subunit casc (41 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Dna (60-mer) (18 kDa, DNA from Escherichia coli)
- Rna (61-mer) (19 kDa, RNA from Escherichia coli)
- Cas5-hnh cascade (400 MDa, Complex from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Crispr system cascade subunit casd (43 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Cryo-EM structure of Cas5-HNH Cascade bound with dsDNA
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 9jxs
Q-score: 0.446
Liu YN, Wang L, Zhang H, Zhu H
To Be Published
- Crispr system cascade subunit casc (41 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Cas5-hnh cascade complex bound with dna (400 MDa, Complex from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Non-target dna (16 kDa, DNA from Escherichia coli)
- Dna (54-mer) (16 kDa, DNA from Escherichia coli)
- Rna (61-mer) (19 kDa, RNA from Escherichia coli)
- Crispr system cascade subunit casd (43 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Magnesium ion (24 Da, Ligand)
- Crispr-associated protein cse2 (crispr_cse2) (20 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Crispr-associated protein cse1 (crispr_cse1) (60 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Crispr-associated endoribonuclease cse3 (31 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Cryo-EM structure of Cas5-HNH Cascade bound with sDNA, Conf1
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8zp7
Q-score: 0.517
Liu YN, Wang L, Zhang H, Zhu H
To Be Published
- Crispr system cascade subunit casc (41 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Dna (60-mer) (18 kDa, DNA from Escherichia coli)
- Rna (61-mer) (19 kDa, RNA from Escherichia coli)
- Crispr-associated protein cse1 (crispr_cse1) (62 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Crispr system cascade subunit casd (43 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Magnesium ion (24 Da, Ligand)
- Cas5-hnh cascade (400 MDa, Complex from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Crispr-associated protein cse2 (crispr_cse2) (20 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
- Crispr-associated endoribonuclease cse3 (31 kDa, Protein from Candidatus Cloacimonetes bacterium ADurb.Bin088)
Cryo-EM structure of Cas8-HNH system at full R-loop state
Resolution: 2.51 Å
EM Method: Single-particle
Fitted PDBs: 8z0k
Q-score: 0.551
Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H
EMBO J (2024) 43 pp. 4656-4667 [ Pubmed: 39251884 DOI: doi:10.1038/s44318-024-00229-8 ]
- Type i-f crispr-associated endoribonuclease cas6/csy4 (20 kDa, Protein from Selenomonas sp.)
- Dna (37-mer) (11 kDa, DNA from Selenomonas sp.)
- Dna (5'-d(p*gp*tp*gp*cp*gp*gp*a)-3') (2 kDa, DNA from Selenomonas sp.)
- Cryo-em structure of cas8-hnh system at full r-loop state (Complex from Selenomonas sp.)
- Hnh endonuclease (39 kDa, Protein from Selenomonas sp.)
- Rna (69-mer) (22 kDa, RNA from Selenomonas sp.)
- Type i-f crispr-associated protein csy3 (37 kDa, Protein from Selenomonas sp.)
- Hypothetical protein j6n51_11000 (28 kDa, Protein from Selenomonas sp.)
Cryo-EM structure of Cas8-HNH system at partial R-loop state
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8z0l
Q-score: 0.549
Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H
EMBO J (2024) 43 pp. 4656-4667 [ Pubmed: 39251884 DOI: doi:10.1038/s44318-024-00229-8 ]
- Type i-f crispr-associated endoribonuclease cas6/csy4 (20 kDa, Protein from Selenomonas sp.)
- Dna (5'-d(p*gp*tp*gp*cp*gp*gp*a)-3') (2 kDa, DNA from Selenomonas sp.)
- Dna (32-mer) (9 kDa, DNA from Selenomonas sp.)
- Cryo-em structure of cas8-hnh system at partial r-loop state (Complex from Selenomonas sp.)
- Hnh endonuclease (39 kDa, Protein from Selenomonas sp.)
- Rna (69-mer) (22 kDa, RNA from Selenomonas sp.)
- Type i-f crispr-associated protein csy3 (37 kDa, Protein from Selenomonas sp.)
- Hypothetical protein j6n51_11000 (28 kDa, Protein from Selenomonas sp.)
Cryo-EM structure of Cas8-HNH system at ssDNA-bound state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8znr
Q-score: 0.505
Li X, Liu Y, Han J, Zhang L, Liu Z, Wang L, Zhang S, Zhang Q, Fu P, Yin H, Zhu H, Zhang H
EMBO J (2024) 43 pp. 4656-4667 [ Pubmed: 39251884 DOI: doi:10.1038/s44318-024-00229-8 ]
- Protein structure (20 kDa, Protein from Selenomonas sp.)
- Rna (56-mer) (22 kDa, RNA from Selenomonas sp.)
- Protein structure (39 kDa, Protein from Selenomonas sp.)
- Protein structure (37 kDa, Protein from Selenomonas sp.)
- Protein structure (28 kDa, Protein from Selenomonas sp.)
- Protein complex (Complex from Selenomonas sp.)
- Dna (35-mer) (10 kDa, DNA from Selenomonas sp.)
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7yrg
Q-score: 0.227
Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z
Mol Cell (2023) 83 pp. 2884-2895.e7 [ Pubmed: 37536340 DOI: doi:10.1016/j.molcel.2023.07.001 ]
- Histone,suv420h1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone methyltransferase and nucleosome complex (Complex)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.2 (12 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- [histone h4]-n-methyl-l-lysine20 n-methyltransferase kmt5b (32 kDa, Protein from Homo sapiens)
- Histone (Complex from Homo sapiens)
Cryo-EM structure of Crt-SPARTA-gRNA-tDNA tetramer (NADase active form)
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8it1
Q-score: 0.271
Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S
Nature (2024) 625 pp. 822-831 [ Pubmed: 37783228 DOI: doi:10.1038/s41586-023-06665-6 ]
- Piwi domain-containing protein (58 kDa, Protein from Thermoflavifilum thermophilum)
- Dna (45-mer) (13 kDa, DNA from synthetic construct)
- Tir domain-containing protein (53 kDa, Protein from Thermoflavifilum thermophilum)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*ap*gp*u)-3') (6 kDa, RNA from synthetic construct)
- The tetramer structural of prokaryotic argonaute with dna and rna complex (Complex from Thermoflavifilum thermophilum)
Cryo-EM structure of Crt-SPARTA-gRNA-tDNA monomer
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8isz
Q-score: 0.321
Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S
Nature (2024) 625 pp. 822-831 [ Pubmed: 37783228 DOI: doi:10.1038/s41586-023-06665-6 ]
- Piwi domain-containing protein (58 kDa, Protein from Thermoflavifilum thermophilum)
- Dna (45-mer) (13 kDa, DNA from synthetic construct)
- Tir domain-containing protein (53 kDa, Protein from Thermoflavifilum thermophilum)
- The dimer structural of prokaryotic argonaute with dna and rna complex (Complex from Thermoflavifilum thermophilum)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*ap*gp*u)-3') (6 kDa, RNA from synthetic construct)
Cryo-EM structure of Crt-SPARTA-gRNA-tDNA dimer (conformation-2)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8it0
Q-score: 0.397
Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S
Nature (2024) 625 pp. 822-831 [ Pubmed: 37783228 DOI: doi:10.1038/s41586-023-06665-6 ]
- Piwi domain-containing protein (58 kDa, Protein from Thermoflavifilum thermophilum)
- Dna (45-mer) (13 kDa, DNA from synthetic construct)
- Tir domain-containing protein (53 kDa, Protein from Thermoflavifilum thermophilum)
- The dimer of prokaryotic argonaute system with dna and rna (Complex from Thermoflavifilum thermophilum)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*ap*gp*u)-3') (6 kDa, RNA from synthetic construct)