Cryo-EM structure of SIR2/HerA antiphage complex
Yu G, Liao F, Li X, Li Z, Zhang H
To Be Published
- Cryo-em structure of sir2/hera complex (400 kDa, Complex from Paenibacillus sp. 453mf)
- Sir2-like domain-containing protein (43 kDa, Protein from Paenibacillus sp. 453mf)
- Helicase hera central domain-containing protein (77 kDa, Protein from Paenibacillus sp. 453mf)
Cryo-EM structure of SIR2/HerA complex
Yu G, Liao F, Li X, Li Z, Zhang H
To Be Published
- Sir2-like domain-containing protein (43 kDa, Protein from Paenibacillus sp. 453mf)
- Cryo-em structure of a bacterial protein (400 kDa, Complex from Paenibacillus sp. 453mf)
- Helicase hera central domain-containing protein (77 kDa, Protein from Paenibacillus sp. 453mf)
Dimer structure of procaryotic Ago
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8k87
Q-score: 0.475
Sun D, Zhu K, Wang L, Mu Z, Wu K, Hua L, Qin B, Gao X, Wang Y, Cui S
Cell Rep (2024) 43 pp. 114391-114391 [ Pubmed: 38923459 DOI: doi:10.1016/j.celrep.2024.114391 ]
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
- Dimmeric gssirt2/ago-gran-tdna complex (Complex from Geobacter sulfurreducens)
- Dna (41-mer) (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Rna/dna (21-mer) (6 kDa, Macromolecule from synthetic construct)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8k88
Q-score: 0.548
Sun D, Zhu K, Wang L, Mu Z, Wu K, Hua L, Qin B, Gao X, Wang Y, Cui S
Cell Rep (2024) 43 pp. 114391-114391 [ Pubmed: 38923459 DOI: doi:10.1016/j.celrep.2024.114391 ]
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
- Short prokaryotic argonaute associated sir2 (120 MDa, Complex from Geobacter sulfurreducens)
- Dna/rna (21-mer) (6 kDa, Macromolecule from synthetic construct)
- Dna (41-mer) (12 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
Cryo-EM structure of the prokaryotic SPARSA system complex
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8jkz
Q-score: 0.475
Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S
Nat Commun (2024) 15 pp. 450-450 [ Pubmed: 38200015 DOI: doi:10.1038/s41467-023-44660-7 ]
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- Sir2/ago (Complex from Geobacter sulfurreducens PCA)
- Ago (Complex)
- Sir2 (Complex from Geobacter sulfurreducens PCA)
Cryo-EM structure of the prokaryotic SPARSA system complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8jl0
Q-score: 0.547
Zhen X, Xu X, Ye L, Xie S, Huang Z, Yang S, Wang Y, Li J, Long F, Ouyang S
Nat Commun (2024) 15 pp. 450-450 [ Pubmed: 38200015 DOI: doi:10.1038/s41467-023-44660-7 ]
- Nicotinamide-adenine-dinucleotide (663 Da, Ligand)
- Piwi domain protein (53 kDa, Protein from Geobacter sulfurreducens)
- The sir2/ago/guide rna/recognition dna complex (Complex from Geobacter sulfurreducens PCA)
- Dna/guide rna duplex (Complex)
- 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*u)-3') (6 kDa, RNA from synthetic construct)
- Ago (Complex)
- Dna (5'-d(p*ap*cp*gp*ap*cp*gp*tp*cp*tp*ap*ap*gp*ap*ap*ap*cp*cp*ap*tp*tp*ap*t)-3') (6 kDa, DNA from synthetic construct)
- Sir2 (Complex from Geobacter sulfurreducens PCA)
- Sir2 superfamily protein (66 kDa, Protein from Geobacter sulfurreducens)
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))