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- PDB-9vji: Cryo-EM structure of apo UL9 complex -

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Basic information

Entry
Database: PDB / ID: 9vji
TitleCryo-EM structure of apo UL9 complex
ComponentsReplication origin-binding protein
KeywordsVIRAL PROTEIN / Helicase ATPase DNA-binding Dimerization
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / DNA replication origin binding / DNA replication / host cell nucleus / ATP binding
Similarity search - Function
Replication origin-binding protein / Origin of replication binding protein / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replication origin-binding protein
Similarity search - Component
Biological speciesHuman alphaherpesvirus 1 strain 17
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsMa, J. / Zhang, X. / Huang, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Virol / Year: 2026
Title: Structure and mechanism of the HSV-1 origin-binding protein UL9.
Authors: Cuiqing Huang / Haiqiang Wu / Jinmiao Song / Xinzheng Zhang / Jun Ma /
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 ...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.
History
DepositionJun 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication origin-binding protein
B: Replication origin-binding protein


Theoretical massNumber of molelcules
Total (without water)194,6642
Polymers194,6642
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Replication origin-binding protein / OBP / OriBP


Mass: 97331.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 strain 17 / Gene: UL9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10193
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-1 UL9-DNA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 190 kDa/nm / Experimental value: NO
Source (natural)Organism: Human herpesvirus 1 (strain 17)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
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: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487model refinement
13RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158949 / Symmetry type: POINT

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