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- PDB-9yc9: HSV replication fork complex bound to pritelivir -

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Basic information

Entry
Database: PDB / ID: 9yc9
TitleHSV replication fork complex bound to pritelivir
Components
  • (DNA (25-MER)) x 2
  • DNA (33-MER)
  • UL30
  • UL42
  • UL5
  • UL52
  • UL8
KeywordsVIRAL PROTEIN / HSV / replisome / replication
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / exonuclease activity / helicase activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed RNA polymerase activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / hydrolase activity ...bidirectional double-stranded viral DNA replication / exonuclease activity / helicase activity / DNA-templated DNA replication / RNA-DNA hybrid ribonuclease activity / DNA-directed RNA polymerase activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / hydrolase activity / nucleotide binding / host cell nucleus / DNA binding / ATP binding
Similarity search - Function
DNA replication helicase domain / DNA helicase/primase complex-associated protein / DNA replication helicase, Herpesvirus / Herpesvirus DNA helicase/primase complex associated protein / DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / Helicase / DNA primase / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol ...DNA replication helicase domain / DNA helicase/primase complex-associated protein / DNA replication helicase, Herpesvirus / Herpesvirus DNA helicase/primase complex associated protein / DNA polymerase processivity factor (UL42) / DNA polymerase processivity factor (UL42) / Helicase / DNA primase / DNA polymerase catalytic subunit Pol, C-terminal / DNA polymerase catalytic subunit Pol / Herpesviridae UL52/UL70 DNA primase / : / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / : / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA polymerase processivity factor / Helicase-primase helicase subunit / Helicase-primase primase subunit / DNA polymerase / DNA helicase/primase complex-associated protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain R-15
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYu, Z. / Abraham, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of HSV replisome
Authors: Yu, Z. / Abraham, J.
History
DepositionSep 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (25-MER)
P: DNA (25-MER)
T: DNA (33-MER)
C: UL52
A: UL5
E: UL30
B: UL8
F: UL42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,18810
Polymers506,7208
Non-polymers4682
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA chain , 3 types, 3 molecules DPT

#1: DNA chain DNA (25-MER)


Mass: 7593.890 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Production host: Homo sapiens (human)
#2: DNA chain DNA (25-MER)


Mass: 7739.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Production host: Homo sapiens (human)
#3: DNA chain DNA (33-MER)


Mass: 10063.456 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Production host: Homo sapiens (human)

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Protein , 5 types, 5 molecules CAEBF

#4: Protein UL52


Mass: 114558.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Gene: UL52 / Production host: Homo sapiens (human) / References: UniProt: A0A5J6DWG4
#5: Protein UL5


Mass: 98823.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Gene: UL5 / Production host: Homo sapiens (human) / References: UniProt: A0A5J6DVR7
#6: Protein UL30


Mass: 136726.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Gene: UL30, HHV1gp046 / Production host: Homo sapiens (human) / References: UniProt: H9E937, DNA-directed DNA polymerase
#7: Protein UL8 / HEPA / Primase-associated factor


Mass: 80005.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Gene: UL8 / Production host: Homo sapiens (human) / References: UniProt: P10192
#8: Protein UL42 / Polymerase accessory protein


Mass: 51207.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain R-15 / Gene: UL42 / Production host: Homo sapiens (human) / References: UniProt: A0A2Z4HDW2

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Non-polymers , 2 types, 2 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-A1BXB / Pritelivir / N-methyl-N-(4-methyl-5-sulfamoyl-1,3-thiazol-2-yl)-2-[4-(pyridin-2-yl)phenyl]acetamide


Mass: 402.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N4O3S2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HSV replisome bound to fork DNA / Type: COMPLEX / Entity ID: #1-#5, #7, #6, #8 / Source: RECOMBINANT
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60000 / Symmetry type: POINT

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