Cryo-EM structure of the NmeCas9-sgRNA-AcrIIC4 ternary complex
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8ja0
Q-score: 0.442
Li X, Liao F, Gao J, Song G, Zhang C, Ji N, Wang X, Wen J, He J, Wei Y, Zhang H, Li Z, Yu G, Yin H
Nucleic Acids Res (2023) 51 pp. 9442-9451 [ DOI: doi:10.1093/nar/gkad669 Pubmed: 37587688 ]
- Crispr-associated endonuclease cas9 (124 kDa, Protein from Neisseria meningitidis)
- Uncharacterized protein (9 kDa, Protein from Haemophilus parainfluenzae)
- Rna (117-mer) (37 kDa, RNA from Neisseria meningitidis)
- A protein complex (Complex from Neisseria meningitidis)
Cryo-EM structure of TIR-APAZ/Ago-gRNA-DNA complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8i87
Q-score: 0.53
Wang X, Li X, Yu G, Zhang L, Zhang C, Wang Y, Liao F, Wen Y, Yin H, Liu X, Wei Y, Li Z, Deng Z, Zhang H
Cell Res (2023) 33 pp. 699-711 [ DOI: doi:10.1038/s41422-023-00839-7 Pubmed: 37311833 ]
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
- Dna (5'-d(p*tp*ap*tp*ap*cp*ap*ap*cp*cp*tp*ap*cp*tp*ap*cp*cp*tp*cp*a)-3') (5 kDa, DNA from Maribacter polysiphoniae)
- Tir-apaz/ago-grna-dna complex (Complex from Maribacter polysiphoniae)
- Magnesium ion (24 Da, Ligand)
- Rna (5'-r(p*up*gp*ap*gp*gp*up*ap*gp*up*ap*gp*gp*up*up*gp*up*ap*up*a)-3') (6 kDa, RNA from Maribacter polysiphoniae)
Cryo-EM structure of TIR-APAZ/Ago-gRNA complex
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8i88
Q-score: 0.433
Wang X, Li X, Yu G, Zhang L, Zhang C, Wang Y, Liao F, Wen Y, Yin H, Liu X, Wei Y, Li Z, Deng Z, Zhang H
Cell Res (2023) 33 pp. 699-711 [ DOI: doi:10.1038/s41422-023-00839-7 Pubmed: 37311833 ]
- Cryo-em structure of tir-apaz/ago-grna complex (Complex from Maribacter polysiphoniae)
- Rna (5'-r(p*gp*a)-3') (629 Da, RNA from Maribacter polysiphoniae)
- Tir domain-containing protein (53 kDa, Protein from Maribacter polysiphoniae)
- Piwi domain-containing protein (58 kDa, Protein from Maribacter polysiphoniae)
Cryo-EM structure of the target ssDNA-bound SIR2-APAZ/Ago-gRNA quaternary complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8in8
Q-score: 0.504
Wang X, Li X, Yu G, Zhang L, Zhang C, Wang Y, Liao F, Wen Y, Yin H, Liu X, Wei Y, Li Z, Deng Z, Zhang H
Cell Res (2023) 33 pp. 699-711 [ DOI: doi:10.1038/s41422-023-00839-7 Pubmed: 37311833 ]
- Dna (5'-d(p*ap*ap*cp*gp*ap*cp*gp*tp*cp*tp*ap*ap*gp*ap*ap*ap*cp*cp*ap*tp*tp*ap*a)-3') (7 kDa, DNA from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Cryo-em structure of the target ssdna-bound sir2-apaz/ago-grna quaternary complex (Complex from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Rna (5'-r(p*ap*up*ap*ap*up*gp*gp*up*up*up*cp*up*up*ap*gp*ap*cp*gp*up*cp*gp*up*up*u)-3') (7 kDa, RNA from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
- Magnesium ion (24 Da, Ligand)
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Structure of the SbCas7-11-crRNA-NTR complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8gna
Q-score: 0.544
Wang X, Yu G, Wen Y, An Q, Li X, Liao F, Lian C, Zhang K, Yin H, Wei Y, Deng Z, Zhang H
Nucleic Acids Res (2022) 50 pp. 12913-12923 [ DOI: doi:10.1093/nar/gkac1151 Pubmed: 36484100 ]
- Rna (5'-r(p*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*gp*u)-3') (14 kDa, RNA from Candidatus Scalindua brodae)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Rna (32-mer) (10 kDa, RNA from Candidatus Scalindua brodae)
- Ternary complex (Complex from Candidatus Scalindua brodae)
Structure of the SbCas7-11-crRNA-NTR-Csx29 complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8gu6
Q-score: 0.496
Wang X, Yu G, Wen Y, An Q, Li X, Liao F, Lian C, Zhang K, Yin H, Wei Y, Deng Z, Zhang H
Nucleic Acids Res (2022) 50 pp. 12913-12923 [ DOI: doi:10.1093/nar/gkac1151 Pubmed: 36484100 ]
- Zinc ion (65 Da, Ligand)
- Ternary complex (Complex from Candidatus Scalindua brodae)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Rna (5'-r(p*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*gp*gp*u)-3') (5 kDa, RNA from Candidatus Scalindua brodae)
- Rna (33-mer) (10 kDa, RNA from Candidatus Scalindua brodae)
- Chat domain protein (82 kDa, Protein from Candidatus Scalindua brodae)
Cryo-EM structure of SbCas7-11 in complex with crRNA and target RNA
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7x7a
Q-score: 0.523
Yu G, Wang X, Zhang Y, An Q, Wen Y, Li X, Yin H, Deng Z, Zhang H
Nat Microbiol (2022) 7 pp. 2078-2088 [ Pubmed: 36302881 DOI: doi:10.1038/s41564-022-01256-z ]
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Rna (33-mer) (10 kDa, RNA from Candidatus Scalindua brodae)
- Binary complex (Complex from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of a bacterial protein
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7x7r
Q-score: 0.384
Yu G, Wang X, Zhang Y, An Q, Wen Y, Li X, Yin H, Deng Z, Zhang H
Nat Microbiol (2022) 7 pp. 2078-2088 [ Pubmed: 36302881 DOI: doi:10.1038/s41564-022-01256-z ]
- Rna (5'-r(p*ap*gp*up*cp*cp*gp*gp*gp*gp*cp*ap*gp*ap*ap*ap*ap*up*up*gp*g)-3') (14 kDa, RNA from Candidatus Scalindua brodae)
- Zinc ion (65 Da, Ligand)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Binary complex (Complex from Candidatus Scalindua brodae)
- Rna (36-mer) (11 kDa, RNA from Candidatus Scalindua brodae)
Cryo-EM structure of a bacterial protein complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7x8a
Q-score: 0.545
Yu G, Wang X, Zhang Y, An Q, Wen Y, Li X, Yin H, Deng Z, Zhang H
Nat Microbiol (2022) 7 pp. 2078-2088 [ Pubmed: 36302881 DOI: doi:10.1038/s41564-022-01256-z ]
- Zinc ion (65 Da, Ligand)
- Complex (Complex from Candidatus Scalindua brodae)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Rna (33-mer) (10 kDa, RNA from Candidatus Scalindua brodae)
- Chat domain protein (82 kDa, Protein from Candidatus Scalindua brodae)
Cryo-EM structure of a bacterial protein complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7xc7
Q-score: 0.423
Yu G, Wang X, Zhang Y, An Q, Wen Y, Li X, Yin H, Deng Z, Zhang H
Nat Microbiol (2022) 7 pp. 2078-2088 [ Pubmed: 36302881 DOI: doi:10.1038/s41564-022-01256-z ]
- Zinc ion (65 Da, Ligand)
- Ramp superfamily protein (197 kDa, Protein from Candidatus Scalindua brodae)
- Chat domain protein (82 kDa, Protein from Candidatus Scalindua brodae)
- Quaternary complex (Complex from Candidatus Scalindua brodae)
- Rna (33-mer) (10 kDa, RNA from Candidatus Scalindua brodae)
- Rna (46-mer) (14 kDa, RNA from Candidatus Scalindua brodae)