Constituent EM map for the consensus map of DdmDE complex
To Be Published
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 ]
- Ddme (79 kDa, Protein from Vibrio cholerae)
- Complementary target dna (7 kDa, DNA from Vibrio cholerae)
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Guide dna (3 kDa, DNA from Vibrio cholerae)
- Non-complementary target dna (short) (3 kDa, DNA from Vibrio cholerae)
- Magnesium ion (24 Da, Ligand)
- Non-complementary target dna (long) (8 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 ]
- Dimeric complex of v. cholerae ddmd bound with ssdna (Complex from Vibrio cholerae)
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
- Ssdna1 (4 kDa, DNA from Vibrio cholerae)
- Ssdna2 (4 kDa, DNA from Vibrio cholerae)
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)
- Monomeric complex of v. cholerae ddmd bound with ssdna (Complex from Vibrio cholerae)
- Ssdna (3 kDa, DNA 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 ]
- Gp13 (10 kDa, Protein from Vibrio cholerae)
- Adaptor gp12 (23 kDa, Protein from Vibrio cholerae)
- Vibrio cholerae phage (Virus from Vibrio cholerae phage)
- Portal gp5 (73 kDa, Protein from Vibrio cholerae)
- Nozzle gp16 (59 kDa, Protein from Vibrio cholerae)
- Ring protein gp10 (26 kDa, Protein from Vibrio cholerae)
portal-tail of Vibrio cholerae typing phage release 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 ]
- Adaptor of release vp1 (23 kDa, Protein from Vibrio cholerae)
- Nozzle of release vp1 (58 kDa, Protein from Vibrio cholerae)
- Vibrio cholerae phage (Virus from Vibrio cholerae phage)
- Portal of release vp1 (66 kDa, Protein from Vibrio cholerae)
- Ring protein of release vp1 (26 kDa, Protein from Vibrio cholerae)
Capsid of Vibrio cholerae 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 ]
- Major capsid of vp1 (43 kDa, Protein from Vibrio cholerae)
- Vibrio cholerae phage (Virus from Vibrio cholerae phage)
- Shp of vp1 (11 kDa, Protein from Vibrio cholerae)