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- PDB-9nda: The rigid portion of Cryo-EM structure of Herpesvirus Helicase-Pr... -

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Basic information

Entry
Database: PDB / ID: 9nda
TitleThe rigid portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex with amenamevir
Components
  • DNA helicase/primase complex-associated protein
  • DNA primase
KeywordsREPLICATION / TRANSFERASE / Inhibitor / Helicase / Primase / Herpesvirus
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / DNA replication / host cell nucleus / zinc ion binding
Similarity search - Function
DNA helicase/primase complex-associated protein / Herpesvirus DNA helicase/primase complex associated protein / DNA primase / Herpesviridae UL52/UL70 DNA primase
Similarity search - Domain/homology
DNA helicase/primase complex-associated protein / DNA primase
Similarity search - Component
Biological speciesHerpesviridae (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYao, Q. / Yu, X.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nat Microbiol / Year: 2025
Title: Structural and mechanistic insights into herpesvirus helicase-primase and its therapeutic inhibitors.
Authors: Qing Yao / Alexandre Mercier / Arabinda Nayak / Lindsey May / Pui Yan Ho / Ariel Lewis-Ballester / Varsha Nair / Annapurna Sapre / Thomas Aeschbacher / Jit Mukherjee / Christopher Richards / ...Authors: Qing Yao / Alexandre Mercier / Arabinda Nayak / Lindsey May / Pui Yan Ho / Ariel Lewis-Ballester / Varsha Nair / Annapurna Sapre / Thomas Aeschbacher / Jit Mukherjee / Christopher Richards / Roberto Mateo / Aesop Cho / Eric Lansdon / Xinchao Yu /
Abstract: The herpes simplex virus (HSV) helicase-primase (HP) complex is a promising anti-herpes therapeutic target. However, progress in developing highly effective small-molecule HP inhibitors (HPIs) for ...The herpes simplex virus (HSV) helicase-primase (HP) complex is a promising anti-herpes therapeutic target. However, progress in developing highly effective small-molecule HP inhibitors (HPIs) for the treatment of genital herpes has been hindered by the lack of structural information on the HP complex and the incomplete understanding of the mechanism of action of HPIs. Here we present the cryogenic electron microscopy structure of the HSV-1 HP apo-complex (3.8 Å), along with structures bound to pritelivir (3.2 Å) and amenamevir (3.2 Å)-two clinically active, chemically distinct HPIs. The potency of both inhibitors against HSV variants bearing mutations within the HPI binding pocket supports the high-resolution mapping of key molecular interactions while revealing residues that govern their antiviral spectrum against alphaherpesviruses. Our results provide important insight into the unique architecture of the HP complex and the mechanism of inhibition of HPIs, paving the way for the development of next-generation antivirals to treat herpesvirus infections.
History
DepositionFeb 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA primase
C: DNA helicase/primase complex-associated protein


Theoretical massNumber of molelcules
Total (without water)194,1322
Polymers194,1322
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 DNA primase


Mass: 114427.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpesviridae (virus) / Gene: UL52 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P10236, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein DNA helicase/primase complex-associated protein / HEPA / Primase-associated factor


Mass: 79704.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpesviridae (virus) / Gene: UL8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10192
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: The ternary complex of HSV-1 helicase-primase complex of UL8/UL52/UL5
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Herpesviridae (virus)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding 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: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 5.84 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115543 / Symmetry type: POINT

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