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 ]
- Phosphonoformic acid (126 Da, Ligand)
- Herpes simplex virus 1 polymerase holoenzyme ul30:ul42 in complex with dna and foscarnet (197 kDa, Complex from Human herpesvirus 1 (strain KOS))
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Primer dna (32-mer) (9 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Dna polymerase (133 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 ]
- Hsv-1 ul42 (Protein from Human alphaherpesvirus 1 strain KOS)
- Template dna (50-mer) (DNA from synthetic construct)
- Primer dna (32-mer) (DNA from synthetic construct)
- Hsv-1 ul30 (Protein from Human alphaherpesvirus 1 strain KOS)
- 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))
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 [ Pubmed: 39197451 DOI: doi:10.1016/j.cell.2024.07.048 ]
- Primer dna (9 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- 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)
- Water (18 Da, Ligand)
- Dna polymerase (133 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Dna polymerase processivity factor (37 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
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 [ Pubmed: 39197451 DOI: doi:10.1016/j.cell.2024.07.048 ]
- Magnesium ion (24 Da, Ligand)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Primer dna (32-mer) (9 kDa, DNA from synthetic construct)
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Water (18 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)
- Dna polymerase (133 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Thymidine-5'-triphosphate (482 Da, Ligand)
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 ]
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Primer dna (33-mer) (10 kDa, DNA from synthetic construct)
- Hsv-1 dna polymerase holoenzyme editing complex (197 kDa, Complex from Human herpesvirus 1 (strain KOS))
- Magnesium ion (24 Da, Ligand)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Dna polymerase (133 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 ]
- Acyclovir triphosphate (465 Da, Ligand)
- Template dna (50-mer) (15 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- 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)
- Primer dna (32-mer) (9 kDa, DNA from synthetic construct)
- Dna polymerase processivity factor (36 kDa, Protein from Human alphaherpesvirus 1 strain KOS)
- Dna polymerase (133 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 polymerase processivity factor (Protein from Human alphaherpesvirus 1 strain KOS)
- Dna template (DNA from synthetic construct)
- Hsv-1 dna polymerase w781v mutant holoenzyme in editing complex (197 kDa, Complex from Human herpesvirus 1 (strain KOS))
- Dna primer (DNA from synthetic construct)
- Dna polymerase (Protein from Human alphaherpesvirus 1 strain KOS)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6m0r
Q-score: 0.467
Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W
Sci Adv (2020) 6 [ DOI: doi:10.1126/sciadv.abb9605 Pubmed: 33028525 ]
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pyrophosphate (177 Da, Ligand)
- V-type proton atpase vo sub-complex (400 MDa, Complex from Saccharomyces cerevisiae)
- V0 assembly protein 1 (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- (6~{e},10~{e},14~{e},18~{e},22~{e},26~{e},30~{r})-2,6,10,14,18,22,26,30-octamethyldotriaconta-2,6,10,14,18,22,26-heptaene (548 Da, Ligand)
- Water (18 Da, Ligand)
- V-type proton atpase subunit a, vacuolar isoform (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Uncharacterized protein ypr170w-b (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c'' (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c' (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6m0s
Q-score: 0.384
Roh SH, Shekhar M, Pintilie G, Chipot C, Wilkens S, Singharoy A, Chiu W
Sci Adv (2020) 6 [ Pubmed: 33028525 DOI: doi:10.1126/sciadv.abb9605 ]
- V-type proton atpase subunit a, vacuolar isoform (94 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase vo sub-complex (400 MDa, Complex from Saccharomyces cerevisiae)
- V0 assembly protein 1 (5 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c'' (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit d (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Uncharacterized protein ypr170w-b (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit c' (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6pv6
Q-score: 0.18
Dashti A, Mashayekhi G, Shekhar M, Ben Hail D, Salah S, Schwander P, des Georges A, Singharoy A, Frank J, Ourmazd A
Nat Commun (2020) 11 pp. 4734-4734 [ DOI: doi:10.1038/s41467-020-18403-x Pubmed: 32948759 ]
- Calcium ion (40 Da, Ligand)
- Ryanodine receptor 1 (502 kDa, Protein from Oryctolagus cuniculus)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)