Herpes simplex virus 1 polymerase holoenzyme bound to DNA and foscarnet (pre-translocation state)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8exx
Q-score: 0.522
Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024) 187 pp. 5572-5586.e15 [ DOI: doi:10.1016/j.cell.2024.07.048 Pubmed: 39197451 ]
- Dna polymerase (133 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Magnesium ion (24 Da, Ligand)
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Primer dna (32-mer) (9 kDa, DNA from synthetic construct)
- Herpes simplex virus 1 polymerase holoenzyme ul30:ul42 in complex with dna and foscarnet (197 kDa, Complex from Human herpesvirus 1 (strain KOS))
- Phosphonoformic acid (126 Da, Ligand)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024) 187 pp. 5572-5586.e15 [ DOI: doi:10.1016/j.cell.2024.07.048 Pubmed: 39197451 ]
- Template dna (50-mer) (DNA from synthetic construct)
- Hsv-1 polymerase holoenzyme ul30:ul42 in complex with template and primer dna (no mismatch), dntp free (197 kDa, Complex from Human herpesvirus 1 (strain KOS))
- Hsv-1 ul30 (Protein from Human alphaherpesvirus 1 strain KOS)
- Hsv-1 ul42 (Protein from Human alphaherpesvirus 1 strain KOS)
- Primer dna (32-mer) (DNA from synthetic construct)
Herpes simplex virus 1 polymerase holoenzyme bound to DNA in both open/closed conformations
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8v1q
Q-score: 0.603
Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024) 187 pp. 5572-5586.e15 [ DOI: doi:10.1016/j.cell.2024.07.048 Pubmed: 39197451 ]
- Dna polymerase (133 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Water (18 Da, Ligand)
- Dna polymerase processivity factor (37 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Herpes simplex virus 1 polymerase holoenzyme ul30:ul42 in complex with template and primer dna strands (Complex from Human herpesvirus 1 (strain KOS))
- Template dna (15 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Primer dna (9 kDa, DNA from synthetic construct)
Herpes simplex virus 1 polymerase holoenzyme bound to DNA and DTTP in closed conformation
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8v1r
Q-score: 0.576
Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024) 187 pp. 5572-5586.e15 [ DOI: doi:10.1016/j.cell.2024.07.048 Pubmed: 39197451 ]
- Dna polymerase (133 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Water (18 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Herpes simplex virus 1 dna polymerase holoenzyme ul30:ul42 bound to dna and dttp (197 kDa, Complex from Human alphaherpesvirus 1 strain KOS)
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Thymidine-5'-triphosphate (482 Da, Ligand)
- Primer dna (32-mer) (9 kDa, DNA from synthetic construct)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
Herpes simplex virus 1 polymerase holoenzyme bound to mismatched DNA in editing conformation
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 8v1s
Q-score: 0.454
Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024) 187 pp. 5572-5586.e15 [ DOI: doi:10.1016/j.cell.2024.07.048 Pubmed: 39197451 ]
- Dna polymerase (133 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Primer dna (33-mer) (10 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Hsv-1 dna polymerase holoenzyme editing complex (197 kDa, Complex from Human herpesvirus 1 (strain KOS))
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8v1t
Q-score: 0.579
Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024) 187 pp. 5572-5586.e15 [ DOI: doi:10.1016/j.cell.2024.07.048 Pubmed: 39197451 ]
- Dna polymerase (133 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Water (18 Da, Ligand)
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Herpes simplex virus type 1 polymerase holoenzyme ul30:ul42 in complex with dsdna and acyclovir triphosphate (197 kDa, Complex from Human alphaherpesvirus 1 strain KOS)
- Magnesium ion (24 Da, Ligand)
- Acyclovir triphosphate (465 Da, Ligand)
- Primer dna (32-mer) (9 kDa, DNA from synthetic construct)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
Herpes simplex virus 1 polymerase W781V mutant holoenzyme bound to DNA in editing conformation
Shankar S, Pan J, Yang P, Bian Y, Oroszlan G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J
Cell (2024) 187 pp. 5572-5586.e15 [ DOI: doi:10.1016/j.cell.2024.07.048 Pubmed: 39197451 ]
- Dna primer (DNA from synthetic construct)
- Hsv-1 dna polymerase w781v mutant holoenzyme in editing complex (197 kDa, Complex from Human herpesvirus 1 (strain KOS))
- Dna polymerase processivity factor (Protein from Human alphaherpesvirus 1 strain KOS)
- Dna polymerase (Protein from Human alphaherpesvirus 1 strain KOS)
- Dna template (DNA from synthetic construct)