Cryo-EM structure of the Cas9d-sgRNA-target DNA complex
Resolution: 2.65 Å
EM Method: Single-particle
Fitted PDBs: 8zdr
Q-score: 0.541
To Be Published
- A protein (Complex from metagenome)
- Zinc ion (65 Da, Ligand)
- Dna (32-mer) (11 kDa, DNA from metagenome)
- Dna (5'-d(p*cp*gp*gp*gp*tp*cp*ap*ap*ap*tp*g)-3') (11 kDa, DNA from metagenome)
- Rna (144-mer) (51 kDa, RNA from metagenome)
- A protein (86 kDa, Protein from metagenome)
Cryo-EM structure of the Cas9d-sgRNA complex
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 8zq9
Q-score: 0.47
To Be Published
- A protein (Complex from metagenome)
- Zinc ion (65 Da, Ligand)
- Rna (128-mer) (51 kDa, RNA from metagenome)
- A protein (86 kDa, Protein from metagenome)
Cryo-EM Structure of MILI(K852A)-piRNA-target (26-nt)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9ij4
Q-score: 0.474
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ Pubmed: 39814893 DOI: doi:10.1038/s41586-024-08438-1 ]
- Mili(k852a)-pirna-target (26-nt) (Complex from Homo sapiens)
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- Rna (25-mer) (8 kDa, RNA from Homo sapiens)
Cryo-EM Structure of MILI-piRNA-target (8-nt)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ij0
Q-score: 0.417
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ Pubmed: 39814893 DOI: doi:10.1038/s41586-024-08438-1 ]
- Rna (5'-r(p*gp*ap*up*gp*gp*up*ap*a)-3') (2 kDa, RNA from Homo sapiens)
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Mili-pirna-target (8-nt) (Complex from Homo sapiens)
Cryo-EM Structure of MILI-piRNA-target (22-nt, bilobed)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9ij1
Q-score: 0.325
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ Pubmed: 39814893 DOI: doi:10.1038/s41586-024-08438-1 ]
- Rna (5'-r(p*cp*ap*ap*gp*up*up*up*cp*cp*ap*up*gp*up*up*gp*ap*up*gp*gp*up*a)-3') (6 kDa, RNA from Homo sapiens)
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Mili-pirna-target (22-nt, bilobed) (Complex from Homo sapiens)
Cryo-EM Structure of MILI-piRNA-target (26-nt)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9ij3
Q-score: 0.463
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ Pubmed: 39814893 DOI: doi:10.1038/s41586-024-08438-1 ]
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Mili-pirna-target (26-nt) (Complex from Homo sapiens)
- Rna (25-mer) (8 kDa, RNA from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
Cryo-EM Structure of MILI(K853A)-piRNA-target
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9ij5
Q-score: 0.461
Li Z, Xu Q, Zhong J, Zhang Y, Zhang T, Ying X, Lu X, Li X, Wan L, Xue J, Huang J, Zhen Y, Zhang Z, Wu J, Shen EZ
Nature (2025) [ Pubmed: 39814893 DOI: doi:10.1038/s41586-024-08438-1 ]
- Mili(k853a)-pirna-target (Complex from Homo sapiens)
- Rna (26-mer) (8 kDa, RNA from Homo sapiens)
- Piwi-like protein 2 (109 kDa, Protein from Mus musculus)
- Magnesium ion (24 Da, Ligand)
- Rna (25-mer) (8 kDa, RNA from Homo sapiens)
Structure of YchF with 50S ribosomal subunit (local map)
To Be Published
- Complex of 50s subunit with ychf (Complex from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s subunit (Complex)
- 23s rrna (partial) (941 kDa, RNA from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Ribosome-binding atpase ychf (41 kDa, Protein from Escherichia coli)
- Ychf (Complex)
Structure of YchF(H114A) on E.coli 50S ribosomal subunit
To Be Published
- 50s subunit (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- Complex of 50s subunit and ychf (Complex)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- Ychf (Complex from Escherichia coli)
- Large ribosomal subunit protein ul11 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- Ribosome-binding atpase ychf (41 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
Cryo-EM structure of CTR-bound type VII CRISPR-Cas complex at post-state I
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8yhd
Q-score: 0.5
Yang J, Li X, He Q, Wang X, Tang J, Wang T, Zhang Y, Yu F, Zhang S, Liu Z, Zhang L, Liao F, Yin H, Zhao H, Deng Z, Zhang H
Nature (2024) 633 pp. 465-472 [ Pubmed: 39143216 DOI: doi:10.1038/s41586-024-07815-0 ]
- A protein (Complex from metagenome)
- Zinc ion (65 Da, Ligand)
- A protein (27 kDa, Protein from metagenome)
- Rna (53-mer) (21 kDa, RNA from metagenome)
- A protein (22 kDa, Protein from metagenome)
- A protein (70 kDa, Protein from metagenome)
- Rna (35-mer) (16 kDa, RNA from metagenome)