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- EMDB-72787: Local refinement of HSV UL5 in amenamevir-bound H/P complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-72787
TitleLocal refinement of HSV UL5 in amenamevir-bound H/P complex
Map data
Sample
  • Complex: HSV helicase-primase complex bound to amenamevir
KeywordsHSV / helicase-primase / HPI / VIRAL PROTEIN
Biological speciesHuman alphaherpesvirus 1 strain R-15
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsYu Z / Abraham J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mechanisms of HSV replisome assembly and targeting by helicase?primase inhibitors
Authors: Yu Z / Abraham J
History
DepositionSep 19, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72787.png

Downloads & links

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Map

FileDownload / File: emd_72787.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0035435606 - 1.9237819
Average (Standard dev.)0.00081064587 (±0.019317465)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72787_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72787_half_map_2.map
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 helicase-primase complex bound to amenamevir

EntireName: HSV helicase-primase complex bound to amenamevir
Components
  • Complex: HSV helicase-primase complex bound to amenamevir

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Supramolecule #1: HSV helicase-primase complex bound to amenamevir

SupramoleculeName: HSV helicase-primase complex bound to amenamevir / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human alphaherpesvirus 1 strain R-15

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 340000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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