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- EMDB-49584: Focused map of UL8-UL52 (410-893) of HSV-1 helicase-primase in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-49584
TitleFocused map of UL8-UL52 (410-893) of HSV-1 helicase-primase in complex with a forked DNA
Map dataFocused map of UL8-UL5(417-890) of HSV-1 helicase-primase in complex with a forked DNA
Sample
  • Complex: HSV-1 helicase-primase in complex with a forked DNA
KeywordsDNA replication / HSV-1 helicase-primase / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 1 strain 17
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsHe Q / Baranovskiy AG / Morstadt LM / Babayeva ND / Lim C / Tahirov TH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM152032 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM150023 United States
CitationJournal: Sci Adv / Year: 2025
Title: Structural basis of herpesvirus helicase-primase inhibition by pritelivir and amenamevir.
Authors: Andrey G Baranovskiy / Qixiang He / Yoshiaki Suwa / Lucia M Morstadt / Nigar D Babayeva / Ci Ji Lim / Tahir H Tahirov /
Abstract: Widespread herpesvirus infections are associated with various diseases. DNA replication of human herpes simplex virus type 1 (HSV-1) requires a helicase-primase (HP) complex of three core proteins: ...Widespread herpesvirus infections are associated with various diseases. DNA replication of human herpes simplex virus type 1 (HSV-1) requires a helicase-primase (HP) complex of three core proteins: UL5, UL52, and UL8. This complex unwinds viral DNA and synthesizes primers for DNA replication, making it an attractive antiviral target. Although HP inhibitors pritelivir and amenamevir were identified through screening, their binding mechanisms remain unclear. Here, we report cryo-electron microscopy structures of HSV-1 HP bound to a forked DNA template alone and in complex with pritelivir or amenamevir. The structures reveal a bilobed architecture highlighting HP coordinated action at the replication fork and providing a structural basis for HP inhibition by illustrating precisely how pritelivir and amenamevir block helicase activity. Data lay a solid foundation for the development of improved antiviral therapies.
History
DepositionMar 5, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49584.png

Downloads & links

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Map

FileDownload / File: emd_49584.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of UL8-UL5(417-890) of HSV-1 helicase-primase in complex with a forked DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.098929115 - 0.31114414
Average (Standard dev.)0.00017032643 (±0.004524168)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharp map of UL8-UL5(417-890) of HSV-1 helicase-primase in...

Fileemd_49584_additional_1.map
AnnotationSharp map of UL8-UL5(417-890) of HSV-1 helicase-primase in complex with a forked DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map-A of UL8-UL5(417-890) of HSV-1 helicase-primase in complex...

Fileemd_49584_half_map_1.map
AnnotationHalf-map-A of UL8-UL5(417-890) of HSV-1 helicase-primase in complex with a forked DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map-B of UL8-UL5(417-890) of HSV-1 helicase-primase in complex...

Fileemd_49584_half_map_2.map
AnnotationHalf-map-B of UL8-UL5(417-890) of HSV-1 helicase-primase in complex with a forked DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HSV-1 helicase-primase in complex with a forked DNA

EntireName: HSV-1 helicase-primase in complex with a forked DNA
Components
  • Complex: HSV-1 helicase-primase in complex with a forked DNA

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Supramolecule #1: HSV-1 helicase-primase in complex with a forked DNA

SupramoleculeName: HSV-1 helicase-primase in complex with a forked DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: HSV-1 helicase-primase in complex with a forked DNA sovled using cryo-EM single-particle analysis
Source (natural)Organism: Human alphaherpesvirus 1 strain 17
Molecular weightTheoretical: 300 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
100.0 mMKClpotassium chloride
0.5 percentGlycerolGlycerol
2.0 mMDTTdithiothreitol
4.0 mMCHAPSOCHAPSO

Details: CHAPSO is made fresh at 80 mM before being added to the sample at a final concentration of 4 mM immediately before vitrification
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12555 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4446980
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: From Cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 431843
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT

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