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)
Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin embedded in lipid bilayer- State 3
Sengupta N, Mondal AK, Mishra S, Chattopadhyay K, Dutta S
J Cell Biol (2021) 220 [ Pubmed: 34617964 DOI: doi:10.1083/jcb.202102035 ]
Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin adhered to liposome membrane surface
Sengupta N, Mondal AK, Mishra S, Chattopadhyay K, Dutta S
J Cell Biol (2021) 220 [ Pubmed: 34617964 DOI: doi:10.1083/jcb.202102035 ]
Cryo-EM 3D reconstruction of Vibrio cholerae Cytolysin partially embedded in lipid bilayer- State 2
Sengupta N, Mondal AK, Mishra S, Chattopadhyay K, Dutta S
J Cell Biol (2021) 220 [ Pubmed: 34617964 DOI: doi:10.1083/jcb.202102035 ]
CryoEM structure of Cascade-TniQ-dsDNA complex
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 6lnb
Q-score: 0.441
Cell Res (2020) 30 pp. 185-187 [ DOI: doi:10.1038/s41422-020-0274-0 Pubmed: 31913359 ]
- Transposition protein tniq (45 kDa, Protein from Vibrio cholerae)
- Target dna strand (51-mer) (15 kDa, DNA from Escherichia coli)
- Crispr-associated protein cas8 (72 kDa, Protein from Vibrio cholerae)
- Cryoem structure of cascade-tniq-dsdna (Complex from Vibrio cholerae)
- Crispr rna (60-mer) (19 kDa, RNA from Vibrio cholerae)
- Non-target dna strand (51-mer) (15 kDa, DNA from Escherichia coli)
- Crispr-associated protein cas7 (40 kDa, Protein from Vibrio cholerae)
- Crispr-associated protein cas6 (23 kDa, Protein from Vibrio cholerae)
CryoEM structure of Cascade-TniQ complex
Resolution: 3.21 Å
EM Method: Single-particle
Fitted PDBs: 6lnc
Q-score: 0.433
Cell Res (2020) 30 pp. 185-187 [ DOI: doi:10.1038/s41422-020-0274-0 Pubmed: 31913359 ]
- Transposition protein tniq (45 kDa, Protein from Vibrio cholerae)
- Crispr-associated protein cas8 (72 kDa, Protein from Vibrio cholerae)
- Crispr rna (60-mer) (19 kDa, RNA from Vibrio cholerae)
- Crispr-associated protein cas7 (40 kDa, Protein from Vibrio cholerae)
- Cryoem structure of cascade-tniq complex (Complex from Vibrio cholerae)
- Crispr-associated protein cas6 (23 kDa, Protein from Vibrio cholerae)
CryoEM structure of VcCascasde-TniQ complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6uvn
Q-score: 0.486
Li Z, Zhang H, Xiao R, Chang L
Cell Res (2020) 30 pp. 179-181 [ Pubmed: 31900425 DOI: doi:10.1038/s41422-019-0268-y ]
- Zinc ion (65 Da, Ligand)
- Crrna (19 kDa, Macromolecule from Vibrio cholerae)
- Protein complex 5 (Complex from Lachnospiraceae bacterium ND2006)
- Cas8/5 (72 kDa, Protein from Vibrio cholerae)
- Tniq (45 kDa, Protein from Vibrio cholerae)
- Cas8_helicalbundle (8 kDa, Protein from Vibrio cholerae)
- Cas6 (25 kDa, Protein from Vibrio cholerae)
- Cas7 (40 kDa, Protein from Vibrio cholerae)