Resolution: 3.5 Å
EM Method: Helical reconstruction
Fitted PDBs: 9ikm
Q-score: 0.422
Cryo-EM structure of Lactobacillus casei DdmE bound with guide and target
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 9iw3
Q-score: 0.438
Huang P, Yan P, Guo L, Fei W, Li Z, Liu J, Kong J, Yao Y, Lu M, Xiao Y, Chen M
Cell Res (2024) 34 pp. 873-876 [ DOI: doi:10.1038/s41422-024-01042-y Pubmed: 39448873 ]
- Dna (5'-d(p*tp*gp*ap*cp*gp*gp*cp*tp*cp*tp*ap*ap*tp*cp*t)-3') (4 kDa, DNA from Lacticaseibacillus)
- Magnesium ion (24 Da, Ligand)
- Dna (25-mer) (7 kDa, DNA from Lacticaseibacillus)
- Dna (5'-d(p*cp*tp*tp*gp*ap*tp*ap*cp*gp*ap*c)-3') (3 kDa, DNA from Lacticaseibacillus)
- Ddme (83 kDa, Protein from Lacticaseibacillus)
- Lactobacillus casei ddme bound with guide and target (Complex from Lacticaseibacillus)
Cryo-EM structure of Lactobacillus casei DdmD dimer bound with DNA
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 9ix4
Q-score: 0.483
Huang P, Yan P, Guo L, Fei W, Li Z, Liu J, Kong J, Yao Y, Lu M, Xiao Y, Chen M
Cell Res (2024) 34 pp. 873-876 [ DOI: doi:10.1038/s41422-024-01042-y Pubmed: 39448873 ]
- Dna (5'-d(p*tp*ap*tp*gp*ap*gp*tp*ap*tp*ap*tp*cp*c)-3') (3 kDa, DNA from Lacticaseibacillus)
- Ddmd (137 kDa, Protein from Lacticaseibacillus)
- Dna (5'-d(p*ap*tp*gp*ap*gp*tp*ap*tp*ap*tp*cp*c)-3') (3 kDa, DNA from Lacticaseibacillus)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (5'-d(p*ap*ap*ap*ap*ap*ap*ap*ap*ap*a)-3') (3 kDa, DNA from Lacticaseibacillus)
- Lactobacillus casei ddmd bound with dna substrate (Complex from Lacticaseibacillus)
Cryo-EM structure of Lactobacillus casei DdmDE bound with DNA
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 9ixm
Q-score: 0.464
Huang P, Yan P, Guo L, Fei W, Li Z, Liu J, Kong J, Yao Y, Lu M, Xiao Y, Chen M
Cell Res (2024) 34 pp. 873-876 [ DOI: doi:10.1038/s41422-024-01042-y Pubmed: 39448873 ]
- Dna (5'-d(p*tp*gp*ap*cp*gp*gp*cp*tp*cp*tp*ap*ap*tp*cp*t)-3') (4 kDa, DNA from Lacticaseibacillus)
- Magnesium ion (24 Da, Ligand)
- Ddmd (137 kDa, Protein from Lacticaseibacillus)
- Ddme (83 kDa, Protein from Lacticaseibacillus)
- Dna (30-mer) (9 kDa, DNA from Lacticaseibacillus)
- Dna (30-mer) (9 kDa, DNA from Lacticaseibacillus)
- Lactobacillus casei ddmde bound with dna (Complex from Lacticaseibacillus)
The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, fully activated
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8z3p
Q-score: 0.42
Li Y, Li Z, Yan P, Hua C, Kong J, Wu W, Cui Y, Duan Y, Li S, Li G, Ji S, Chen Y, Zhao Y, Yang P, Hu C, Lu M, Chen M, Xiao Y
Science (2024) pp. eadr0393-eadr0393 [ Pubmed: 39666823 DOI: doi:10.1126/science.adr0393 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine deaminase domain-containing protein (69 kDa, Protein from Limisphaera ngatamarikiensis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Caad:ca6:atp 6:3:6 (Complex from Limisphaera ngatamarikiensis)
- Zinc ion (65 Da, Ligand)
- Rna (5'-r(p*ap*ap*ap*ap*ap*a)-3') (1 kDa, RNA from Limisphaera ngatamarikiensis)
The structure of type III CRISPR-associated deaminase in complex cA4
Resolution: 2.28 Å
EM Method: Single-particle
Fitted PDBs: 8z3r
Q-score: 0.605
Li Y, Li Z, Yan P, Hua C, Kong J, Wu W, Cui Y, Duan Y, Li S, Li G, Ji S, Chen Y, Zhao Y, Yang P, Hu C, Lu M, Chen M, Xiao Y
Science (2024) pp. eadr0393-eadr0393 [ Pubmed: 39666823 DOI: doi:10.1126/science.adr0393 ]
- Crispr-associated adenosine deaminase (Complex from Limisphaera ngatamarikiensis)
- 3'-o-[(r)-{[(2s,3as,4s,6s,6as)-6-(6-amino-9h-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2h-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine (658 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Adenosine deaminase domain-containing protein (70 kDa, Protein from Limisphaera ngatamarikiensis)