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- PDB-9nee: The flexible portion of Cryo-EM structure of Herpesvirus Helicase... -

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Basic information

Entry
Database: PDB / ID: 9nee
TitleThe flexible portion of Cryo-EM structure of Herpesvirus Helicase-Primase complex with Pritelivir
Components
  • DNA primase
  • DNA replication helicase
KeywordsREPLICATION / TRANSFERASE/INHIBITOR / Inhibitor / Herpesvirus / Helicase / Primase / Pritelivir / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA-directed RNA polymerase activity / DNA replication / hydrolase activity / host cell nucleus / zinc ion binding / ATP binding
Similarity search - Function
DNA replication helicase domain / DNA replication helicase, Herpesvirus / Helicase / DNA primase / Herpesviridae UL52/UL70 DNA primase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA replication helicase / DNA primase
Similarity search - Component
Biological speciesHerpesviridae (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYao, Q. / Yu, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure and Inhibition Mechanism of Herpesvirus Helicase-Primase
Authors: Yao, Q. / Mercier, A.
History
DepositionFeb 19, 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: Mask / Part number: 1 / Data content type: Mask / 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

Downloads & links

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Assembly

Deposited unit
A: DNA primase
B: DNA replication helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,0753
Polymers209,6732
Non-polymers4021
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: 114544.531 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 replication helicase


Mass: 95128.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpesviridae (virus) / Gene: HELI, UL5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P10189, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Chemical ChemComp-A1BXB / Pritelivir / N-methyl-N-(4-methyl-5-sulfamoyl-1,3-thiazol-2-yl)-2-[4-(pyridin-2-yl)phenyl]acetamide


Mass: 402.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18N4O3S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: The ternary complex of HSV-1 UL8/UL52/UL5 helicase-primase complex
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: 100 µm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
11RELION5final Euler assignment
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136652 / Symmetry type: POINT

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