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)
DdmD dimer in complex with ssDNA
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 8u0u
Q-score: 0.479
Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW
Nature (2024) 630 pp. 961-967 [ DOI: doi:10.1038/s41586-024-07515-9 Pubmed: 38740055 ]
- Helicase/uvrb n-terminal domain-containing protein (Complex from Vibrio cholerae)
- Dna (Complex)
- Ddmd (Complex)
- Dna (5'-d(p*tp*tp*ap*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from synthetic construct)
- Helicase/uvrb n-terminal domain-containing protein (136 kDa, Protein from Vibrio cholerae)
DdmD monomer in complex with ssDNA
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8u0w
Q-score: 0.489
Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW
Nature (2024) 630 pp. 961-967 [ DOI: doi:10.1038/s41586-024-07515-9 Pubmed: 38740055 ]
- Ddmd (Complex from Vibrio cholerae)
- Dna (5'-d(p*tp*tp*ap*tp*tp*tp*tp*tp*tp*tp*tp*t)-3') (3 kDa, DNA from synthetic construct)
- Helicase/uvrb n-terminal domain-containing protein (140 kDa, Protein from Vibrio cholerae)
DdmE in complex with guide and target DNA
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8u0j
Q-score: 0.459
Bravo JPK, Ramos DA, Fregoso Ocampo R, Ingram C, Taylor DW
Nature (2024) 630 pp. 961-967 [ DOI: doi:10.1038/s41586-024-07515-9 Pubmed: 38740055 ]
- Dna (5'-d(p*gp*tp*tp*ap*gp*ap*cp*tp*tp*tp*ap*ap*gp*t)-3') (4 kDa, DNA from synthetic construct)
- Ddme (78 kDa, Protein from Vibrio cholerae)
- Dna (5'-d(p*ap*cp*tp*tp*ap*ap*ap*gp*tp*cp*tp*ap*ap*cp*cp*tp*ap*tp*ap*gp*gp*ap*t)-3') (7 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Ddme (211 kDa, Complex from Streptococcus pyogenes)
- Dna (5'-d(p*ap*tp*cp*cp*tp*ap*tp*ap*gp*gp*a)-3') (3 kDa, DNA from synthetic construct)
CryoEM structure of Vibrio cholerae transposon Tn6677 AAA+ ATPase TnsC
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7rzy
Q-score: 0.09
Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernandez IS, Sternberg SH
Nature (2022) 609 pp. 384-393 [ DOI: doi:10.1038/s41586-022-05059-4 Pubmed: 36002573 ]
- Tn6677 vibrio cholerae transposon tnsc (vchtnsc) (37 kDa, Protein from Vibrio cholerae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Vchtnsc (238 kDa, Complex from Vibrio cholerae)
VchTnsC AAA+ ATPase with DNA, single heptamer
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ufi
Q-score: 0.321
Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernandez IS, Sternberg SH
Nature (2022) 609 pp. 384-393 [ DOI: doi:10.1038/s41586-022-05059-4 Pubmed: 36002573 ]
- Vchtnsc aaa+ atpase with atp and dna (single heptamer form) (Complex from Vibrio cholerae)
- Dna (5'-d(p*cp*tp*cp*cp*ap*gp*tp*ap*cp*ap*gp*cp*gp*cp*gp*gp*cp*tp*gp*ap*a)-3') (6 kDa, DNA from synthetic construct)
- Dna (5'-d(p*tp*tp*cp*ap*gp*cp*cp*gp*cp*gp*cp*tp*gp*tp*ap*cp*tp*gp*gp*ap*g)-3') (6 kDa, DNA from synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Vchtnsc (35 kDa, Protein from Vibrio cholerae)
VchTnsC AAA+ with DNA (double heptamer)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 7ufm
Q-score: 0.197
Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernandez IS, Sternberg SH
Nature (2022) 609 pp. 384-393 [ DOI: doi:10.1038/s41586-022-05059-4 Pubmed: 36002573 ]
- Vchtnsc (35 kDa, Protein from Vibrio cholerae)
- Dna (36-mer) (11 kDa, DNA from synthetic construct)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Vchtnsc aaa+ with dna (double heptamer) (Complex from Vibrio cholerae)
- Dna (36-mer) (11 kDa, DNA from synthetic construct)