9NN2 | pdb_00009nn2

Composite structure of HSV-1 helicase-primase in complex with a forked DNA and amenamevir


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of herpesvirus helicase-primase inhibition by pritelivir and amenamevir.

Baranovskiy, A.G.He, Q.Suwa, Y.Morstadt, L.M.Babayeva, N.D.Lim, C.J.Tahirov, T.H.

(2025) Sci Adv 11: eadz1989-eadz1989

  • DOI: https://doi.org/10.1126/sciadv.adz1989
  • Primary Citation of Related Structures:  
    9NN2, 9NNP, 9NQP

  • PubMed Abstract: 

    Widespread herpesvirus infections are associated with various diseases. DNA replication of human herpes simplex virus type 1 (HSV-1) requires a helicase-primase (HP) complex of three core proteins: UL5, UL52, and UL8. This complex unwinds viral DNA and synthesizes primers for DNA replication, making it an attractive antiviral target. Although HP inhibitors pritelivir and amenamevir were identified through screening, their binding mechanisms remain unclear. Here, we report cryo-electron microscopy structures of HSV-1 HP bound to a forked DNA template alone and in complex with pritelivir or amenamevir. The structures reveal a bilobed architecture highlighting HP coordinated action at the replication fork and providing a structural basis for HP inhibition by illustrating precisely how pritelivir and amenamevir block helicase activity. Data lay a solid foundation for the development of improved antiviral therapies.


  • Organizational Affiliation
    • Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication helicaseB [auth A]852Human 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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primaseC [auth B]1,058Human 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  
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UniProt GroupP10236
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA helicase/primase complex-associated proteinD [auth C]750Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: UL8
UniProt
Find proteins for P10192 (Human herpesvirus 1 (strain 17))
Explore P10192 
Go to UniProtKB:  P10192
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10192
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*CP*TP*GP*TP*T)-3')A [auth D]43Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21_5207:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM152032
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM150023

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release