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 ]
- Ddmd (137 kDa, Protein 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)
- Dna (5'-d(p*tp*ap*tp*gp*ap*gp*tp*ap*tp*ap*tp*cp*c)-3') (3 kDa, DNA from Lacticaseibacillus)
- Lactobacillus casei ddmd bound with dna substrate (Complex from Lacticaseibacillus)
- Dna (5'-d(p*ap*tp*gp*ap*gp*tp*ap*tp*ap*tp*cp*c)-3') (3 kDa, DNA 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 ]
- Ddmd (137 kDa, Protein from Lacticaseibacillus)
- Dna (30-mer) (9 kDa, DNA from Lacticaseibacillus)
- Ddme (83 kDa, Protein from Lacticaseibacillus)
- Magnesium ion (24 Da, Ligand)
- 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)
- Lactobacillus casei ddmde bound with dna (Complex from Lacticaseibacillus)
- Dna (30-mer) (9 kDa, DNA 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 [ DOI: doi:10.1126/science.adr0393 Pubmed: 39666823 ]
- Adenosine deaminase domain-containing protein (69 kDa, Protein from Limisphaera ngatamarikiensis)
- Zinc ion (65 Da, Ligand)
- Caad:ca6:atp 6:3:6 (Complex from Limisphaera ngatamarikiensis)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 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 [ DOI: doi:10.1126/science.adr0393 Pubmed: 39666823 ]
- Crispr-associated adenosine deaminase (Complex from Limisphaera ngatamarikiensis)
- Zinc ion (65 Da, Ligand)
- Adenosine deaminase domain-containing protein (70 kDa, Protein 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)
Resolution: 2.68 Å
EM Method: Single-particle
Fitted PDBs: 9ekf
Q-score: 0.597
Morano NC, Guo Y, Becker JE, Li Z, Yu J, Ho DD, Shapiro L, Kwong PD
Structure (2025) 33 pp. 228-233.e3 [ Pubmed: 39884273 DOI: doi:10.1016/j.str.2025.01.001 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab 65c6 light chain (23 kDa, Protein from Homo sapiens)
- Complex of hemagglutinin from h5n1 ha a/texas/37/2024 with antibody (360 kDa, Complex from Homo sapiens)
- Fab 65c6 heavy chain (25 kDa, Protein from Homo sapiens)
- Hemagglutinin (65 kDa, Protein from Influenza A virus)
The structure of type III CRISPR-associated deaminase in complex 2cA6 and 2ATP, partial activated
Resolution: 3.19 Å
EM Method: Single-particle
Fitted PDBs: 8z3k
Q-score: 0.425
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 [ DOI: doi:10.1126/science.adr0393 Pubmed: 39666823 ]
- Crispr-associated adenosine deaminase (Complex from Limisphaera ngatamarikiensis)
- Zinc ion (65 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Adenosine deaminase domain-containing protein (70 kDa, Protein from Limisphaera ngatamarikiensis)
- 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 apo form
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8z40
Q-score: 0.464
Resolution: 3.22 Å
EM Method: Helical reconstruction
Fitted PDBs: 9ikj
Q-score: 0.53
Wang T, Li Z, Xu K, Huang W, Huang G, Zhang QC, Yan N
PNAS (2024) 121 pp. e2417046121-e2417046121 [ DOI: doi:10.1073/pnas.2417046121 Pubmed: 39382995 ]
- Tlp-1a (Complex from algae metagenome)
- Tlp-1 (25 kDa, Protein from algae metagenome)
Resolution: 3.51 Å
EM Method: Helical reconstruction
Fitted PDBs: 9ikk
Q-score: 0.452
Wang T, Li Z, Xu K, Huang W, Huang G, Zhang QC, Yan N
PNAS (2024) 121 pp. e2417046121-e2417046121 [ DOI: doi:10.1073/pnas.2417046121 Pubmed: 39382995 ]
- Tlp-2 (25 kDa, Protein from algae metagenome)
- Tlp-1b (Complex from algae metagenome)
Cryo-EM structure of a bacterial protein
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8wiv
Q-score: 0.411
Yu G, Liao F, Li X, Li Z, Zhang H
To Be Published
- Magnesium ion (24 Da, Ligand)
- Phosphothiophosphoric acid-adenylate ester (523 Da, Ligand)
- 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)