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)
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 [ Pubmed: 33028525 DOI: doi:10.1126/sciadv.abb9605 ]
- Water (18 Da, Ligand)
- 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))
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- (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)
- V-type proton atpase subunit e (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit a, vacuolar isoform (94 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 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))
- Pyrophosphate (177 Da, Ligand)
- V-type proton atpase subunit d (39 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 ]
- 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 e (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- V-type proton atpase subunit a, vacuolar isoform (94 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 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))
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 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Ryanodine receptor 1 (502 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7jmf
Q-score: 0.11
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 ]
- Peptidyl-prolyl cis-trans isomerase fkbp1b (11 kDa, Protein from Homo sapiens)
- Ryanodine receptor 1 (502 kDa, Protein from Oryctolagus cuniculus)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ryanodine receptor 1 bound to fkbp1b (2 MDa, Complex from Oryctolagus cuniculus)