9VLQ | pdb_00009vlq

herpes simplex virus type 1 helicase-primase structure in complex with ssDNA, ADP and magnesium ion


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structural and mechanistic insights into the herpes simplex virus type 1 helicase-primase primosome.

Wu, Y.Jiang, Z.Chen, X.Li, D.Zhang, Z.Dong, C.

(2025) Cell Discov 11: 100-100

  • DOI: https://doi.org/10.1038/s41421-025-00855-4
  • Primary Citation of Related Structures:  
    9VLQ

  • PubMed 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 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 2+ 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.


  • Organizational Affiliation
    • Department of Thyroid and Breast Surgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication helicase907Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: HELIUL5
EC: 3.6.4
UniProt
Find proteins for P10189 (Human herpesvirus 1 (strain 17))
Explore P10189 
Go to UniProtKB:  P10189
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10189
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Helicase-primase subunit775Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: UL8
UniProt
Find proteins for G8HBC1 (Human herpesvirus 1 (strain 17))
Explore G8HBC1 
Go to UniProtKB:  G8HBC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8HBC1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase1,058Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: UL52
EC: 2.7.7
UniProt
Find proteins for P10236 (Human herpesvirus 1 (strain 17))
Explore P10236 
Go to UniProtKB:  P10236
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10236
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (44-MER)D [auth X]44ssDNA virus sp.
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC4.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release