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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: To Be Published
Title: Structure and Inhibition Mechanism of Herpesvirus Helicase-Primase
Authors: Yao, Q. / Mercier, A.
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
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary 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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