9VJH | pdb_00009vjh

Cryo-EM structure of UL9-DNA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structure and mechanism of the HSV-1 origin-binding protein UL9.

Huang, C.Wu, H.Song, J.Zhang, X.Ma, J.

(2026) J Virol : e0027126-e0027126

  • DOI: https://doi.org/10.1128/jvi.00271-26
  • Primary Citation Related Structures: 
    9VJH, 9VJI

  • PubMed Abstract: 

    The herpesvirus DNA replication machinery comprises a battery of viral enzymes that orchestrate viral genome synthesis. In herpes simplex virus type 1 (HSV-1), the machinery consists of seven essential components, including the origin-binding protein UL9, the single-stranded DNA (ssDNA)-binding protein ICP8, the heterodimeric DNA polymerase complex UL30-UL42, and the heterotrimeric helicase-primase complex UL5-UL8-UL52. UL9, a superfamily 2 (SF2) helicase, functions as a dimer that specifically recognizes replication origins and unwinds duplex DNA to initiate replication. Furthermore, UL9 recruits the replication machinery through interactions with viral components and engages cellular proteins that regulate its function. However, the molecular mechanisms underlying the multifunctionality of UL9 remain incompletely understood due to the lack of structural information. Here, we present cryo-electron microscopy structures of UL9 in both apo and DNA-bound states. Together with biochemical and enzymatic assays, we elucidate the molecular basis of UL9 dimerization, origin recognition and allosteric regulation by ICP8.IMPORTANCEHerpes simplex virus 1 (HSV-1) is a widespread virus that causes lifelong infections, leading to periodic outbreaks ranging from common cold sores to life-threatening encephalitis, and no current treatment can eradicate the dormant virus. To multiply, HSV-1 relies on a protein-based molecular machine to replicate its genome, where the unwinding of double-stranded DNA at specific replication origins is coordinated by the viral origin-binding protein UL9. Here, we present the high-resolution structures of UL9, both alone and bound to DNA, revealing how it forms a stable homodimer to grab onto the origin. Combined with precise biochemical experiments, we further show how UL9 collaborates with another viral helper protein, ICP8, to unwind DNA efficiently. These discoveries solve a long-standing puzzle in herpesvirus biology and offer a vital structural blueprint for designing new antiviral drugs that can block viral replication at its very earliest stage.


  • Organizational Affiliation
    • State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 222.91 kDa 
  • Atom Count: 13,958 
  • Modeled Residue Count: 1,632 
  • Deposited Residue Count: 1,852 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Replication origin-binding protein
A, B
880Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: UL9
UniProt
Find proteins for P10193 (Human herpesvirus 1 (strain 17))
Explore P10193 
Go to UniProtKB:  P10193
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10193
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*GP*CP*GP*TP*TP*CP*GP*CP*AP*CP*TP*TP*CP*GP*TP*CP*CP*CP*AP*AP*TP*A)-3')C,
D [auth E]
23Human alphaherpesvirus 1 strain 17
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*TP*TP*GP*GP*GP*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*CP*GP*CP*T)-3')E [auth D],
F
23Human alphaherpesvirus 1 strain 17
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release
  • Version 1.1: 2026-08-19
    Changes: Data collection, Database references