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- EMDB-65680: Cryo-EM map of ASFV DNA polymerase in apo state 2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-65680
TitleCryo-EM map of ASFV DNA polymerase in apo state 2
Map data
Sample
  • Virus: African swine fever virus
KeywordsASFV / DNA polymerase beta / DNA BINDING PROTEIN
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsHu Z / Yan R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Iscience / Year: 2025
Title: Structural basis for DNA replication by the African swine fever virus polymerase
Authors: Hu Z / SunKang Y / Liu Z / Huang L / Qi W / Yan R
History
DepositionAug 4, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65680.png

Downloads & links

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Map

FileDownload / File: emd_65680.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 270 pix.
= 223.29 Å		0.83 Å/pix.
x 270 pix.
= 223.29 Å		0.83 Å/pix.
x 270 pix.
= 223.29 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.2278767 - 3.5106206
Average (Standard dev.)0.000052067888 (±0.05931718)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 223.29001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65680_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_65680_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 : African swine fever virus

EntireName: African swine fever virus
Components
  • Virus: African swine fever virus

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Supramolecule #1: African swine fever virus

SupramoleculeName: African swine fever virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10497 / Sci species name: African swine fever virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 364465
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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