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- PDB-9ycv: HSV Helicase-primase complex bound to amenamevir -

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Basic information

Entry
Database: PDB / ID: 9ycv
TitleHSV Helicase-primase complex bound to amenamevir
Components
  • DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')
  • UL5
  • UL52
  • UL8
KeywordsVIRAL PROTEIN / HSV / helicase-primase / HPI
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / helicase activity / DNA-directed RNA polymerase activity / DNA replication / hydrolase activity / host cell nucleus / 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 / Helicase / DNA primase / Herpesviridae UL52/UL70 DNA primase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / Helicase-primase helicase subunit / Helicase-primase primase subunit / DNA helicase/primase complex-associated protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain R-15
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsYu, Z. / Abraham, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mechanisms of HSV replisome assembly and targeting by helicase?primase inhibitors
Authors: Yu, Z. / Abraham, J.
History
DepositionSep 19, 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: 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

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Assembly

Deposited unit
D: DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')
C: UL52
A: UL5
B: UL8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,7166
Polymers295,1684
Non-polymers5482
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 , 1 types, 1 molecules D

#1: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*T)-3')


Mass: 1780.199 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 , 3 types, 3 molecules CAB

#2: 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
#3: 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
#4: 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

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-A1BXD / Amenamevir


Mass: 482.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N4O5S / 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 helicase-primase complex bound to amenamevir / Type: COMPLEX / Entity ID: #1-#4 / 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: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 340000 / Symmetry type: POINT

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