Structure of DdmD dimer with ssDNA with ADP bound
Nucleic Acids Res (2025) 53 [ Pubmed: 39907109 DOI: doi:10.1093/nar/gkaf064 ]
- Dna (5'-d(p*cp*cp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from synthetic construct)
- Dna (5'-d(p*cp*tp*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from synthetic construct)
- Ddmd dimer with ssdna without nucleotide (300 kDa, Complex from Vibrio cholerae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
Structure of V.cholera DdmDE (2D:1E) in complex with DNA
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 9bgk
Q-score: 0.412
Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM
Cell (2024) 187 pp. 5253-5266.e16 [ DOI: doi:10.1016/j.cell.2024.07.028 Pubmed: 39173632 ]
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Ddme (79 kDa, Protein from Vibrio cholerae)
- Non-complementary target dna (short) (3 kDa, DNA from Vibrio cholerae)
- Non-complementary target dna (long) (8 kDa, DNA from Vibrio cholerae)
- Magnesium ion (24 Da, Ligand)
- Guide dna (3 kDa, DNA from Vibrio cholerae)
- Complementary target dna (7 kDa, DNA from Vibrio cholerae)
- Ddmd dimer bind ddme in complex with dna (Complex from Vibrio cholerae)
Structure of V. cholerae DdmD in complex with ssDNA
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 9bf5
Q-score: 0.455
Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM
Cell (2024) 187 pp. 5253-5266.e16 [ DOI: doi:10.1016/j.cell.2024.07.028 Pubmed: 39173632 ]
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Ssdna1 (4 kDa, DNA from Vibrio cholerae)
- Dimeric complex of v. cholerae ddmd bound with ssdna (Complex from Vibrio cholerae)
- Ssdna2 (4 kDa, DNA from Vibrio cholerae)
Vibrio cholerae DdmD-DdmE holo complex
Loeff L, Adams DW, Chanez C, Stutzmann S, Righi L, Blokesch M, Jinek M
Science (2024) 385 pp. 188-194 [ Pubmed: 38870273 DOI: doi:10.1126/science.adq0534 ]
- Target dna strand (20 kDa, DNA from synthetic construct)
- Ddmd-ddme holocomplex (Complex from Vibrio cholerae)
- Vibrio cholerae ddme (79 kDa, Protein from Vibrio cholerae)
- Non-target dna strand (20 kDa, DNA from synthetic construct)
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Magnesium ion (24 Da, Ligand)
- 14 nucleotide dna guide with terminal 5' phosphate (4 kDa, DNA from synthetic construct)
Structure of apo-state V. cholerae DdmD
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9bf1
Q-score: 0.023
Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM
Cell (2024) 187 pp. 5253-5266.e16 [ DOI: doi:10.1016/j.cell.2024.07.028 Pubmed: 39173632 ]
Structure of V. cholerae monomeric DdmD bound with ssDNA
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 9c6q
Q-score: 0.386
Yang XY, Shen Z, Wang C, Nakanishi K, Fu TM
Cell (2024) 187 pp. 5253-5266.e16 [ DOI: doi:10.1016/j.cell.2024.07.028 Pubmed: 39173632 ]
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Ssdna (3 kDa, DNA from Vibrio cholerae)
- Monomeric complex of v. cholerae ddmd bound with ssdna (Complex from Vibrio cholerae)
Portal-tail of Vibrio cholerae typing phage mature VP1
Pang H, Fan F, Zheng J, Xiao H, Tan Z, Song J, Kan B, Liu H
Structure (2024) 32 pp. 2364-2374.e2 [ Pubmed: 39471801 DOI: doi:10.1016/j.str.2024.10.005 ]
- Vibrio cholerae phage (Virus from Vibrio cholerae phage)
- Nozzle gp16 (59 kDa, Protein from Vibrio cholerae)
- Adaptor gp12 (23 kDa, Protein from Vibrio cholerae)
- Gp13 (10 kDa, Protein from Vibrio cholerae)
- Portal gp5 (73 kDa, Protein from Vibrio cholerae)
- Ring protein gp10 (26 kDa, Protein from Vibrio cholerae)