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- PDB-9vlq: herpes simplex virus type 1 helicase-primase structure in complex... -

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Basic information

Entry
Database: PDB / ID: 9vlq
Titleherpes simplex virus type 1 helicase-primase structure in complex with ssDNA, ADP and magnesium ion
Components
  • DNA (44-MER)
  • DNA primase
  • DNA replication helicase
  • Helicase-primase subunit
KeywordsREPLICATION/DNA / herpes simplex virus type 1 / helicase / primase / UL5 / UL52 / UL8 / DNA replication / Helicase superfamily I / SF1 / REPLICATION-DNA complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / viral genome replication / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / DNA replication / hydrolase activity / host cell nucleus / zinc ion 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 / Helicase / DNA primase / Herpesviridae UL52/UL70 DNA primase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / Helicase-primase subunit / DNA replication helicase / DNA primase
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
ssDNA virus sp.
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWu, Y.Q. / Jiang, Z.Y. / Chen, X.L. / Zheng, Z.Y. / Dong, C.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Discov / Year: 2025
Title: Structural and mechanistic insights into the herpes simplex virus type 1 helicase-primase primosome.
Authors: Yaqi Wu / Ziyi Jiang / Xiaoling Chen / Danyang Li / Zhengyu Zhang / Changjiang Dong /
Abstract: DNA unwinding and primer synthesis are fundamental processes in genome replication. The human herpes simplex virus type 1 (HSV-1) helicase-primase forms a unique heterotrimeric primosome that is ...DNA unwinding and primer synthesis are fundamental processes in genome replication. The human herpes simplex virus type 1 (HSV-1) helicase-primase forms a unique heterotrimeric primosome that is essential for viral DNA unwinding and primer synthesis and represents an ideal drug target. However, its molecular mechanism remains poorly understood. Here we report the cryo-electron microscopic structure of the primosome in complex with single-stranded DNA, ADP and Mg to 3.47 Å resolution, which reveals that the primosome forms an unprecedented architecture in a fully open DNA binding groove between the helicase domains 1A and 2A-2B and that the primase subunit UL52 interacts extensively with the helicase subunit UL5 and accessory protein subunit UL8. Integrating mutagenesis, biochemical assays, structural analysis and 3D variability display analysis, we have identified the active sites of the ATPase, helicase and primase and critical interfaces between UL52, UL5 and UL8. Our work suggests that the primosome unwinds and translocates DNA via bidirectional rotation, and proposes a mechanistic model for DNA-dependent ATPase activation and alternating activity between helicase and primase. Herpesviridae family viruses pose significant threats to human health worldwide, and this trimeric assembly of primosomes is conserved. Our work provides a framework for understanding replication mechanisms across related viruses and for the rational design of broad-spectrum antivirals.
History
DepositionJun 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data 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
A: DNA replication helicase
B: Helicase-primase subunit
C: DNA primase
X: DNA (44-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,4026
Polymers312,9514
Non-polymers4522
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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Protein , 3 types, 3 molecules ABC

#1: Protein DNA replication helicase


Mass: 101903.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: HELI, UL5
Production host: Insect expression vector pBlueBachsGCA1 (others)
References: UniProt: P10189, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Helicase-primase subunit


Mass: 83085.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL8
Production host: Insect expression vector pBlueBachsGCA1 (others)
References: UniProt: G8HBC1
#3: Protein DNA primase


Mass: 114558.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL52
Production host: Insect expression vector pBlueBachsGCA1 (others)
References: UniProt: P10236, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 1 types, 1 molecules X

#4: DNA chain DNA (44-MER)


Mass: 13402.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ssDNA virus sp.

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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-1 helicase-primase in complex with ssDNA, ADP and magnesium
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Source (recombinant)Organism: Insect expression vector pBlueBachsGCA1 (others)
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: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
9PHENIX1.20.1_4487model refinement
12cryoSPARC4classification
13cryoSPARC43D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35958 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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