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- EMDB-39529: ASFV RNA polymerase-M1249L complex 24 -

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Basic information

Entry
Database: EMDB / ID: EMD-39529
TitleASFV RNA polymerase-M1249L complex 24
Map data
Sample
  • Complex: African swine fever virus RNA polymerase complex
KeywordsASFV / RNA polymerase / VIRAL PROTEIN
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsFeng XY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Transcription regulation of African swine fever virus: dual role of M1249L.
Authors: Dongming Zhao / Nan Wang / Xiaoying Feng / Zhenjiang Zhang / Kongen Xu / Tao Zheng / Yunge Yang / Xuemei Li / Xianjin Ou / Rui Zhao / Zihe Rao / Zhigao Bu / Yutao Chen / Xiangxi Wang /
Abstract: African swine fever virus (ASFV), which poses significant risks to the global economy, encodes a unique host-independent transcription system. This system comprises an eight-subunit RNA polymerase ...African swine fever virus (ASFV), which poses significant risks to the global economy, encodes a unique host-independent transcription system. This system comprises an eight-subunit RNA polymerase (vRNAP), temporally expressed transcription factors and transcript associated proteins, facilitating cross-species transmission via intermediate host. The protein composition of the virion and the presence of transcription factors in virus genome suggest existence of distinct transcription systems during viral infection. However, the precise mechanisms of transcription regulation remain elusive. Through analyses of dynamic transcriptome, vRNAP-associated components and cell-based assay, the critical role of M1249L in viral transcription regulation has been highlighted. Atomic-resolution structures of vRNAP-M1249L supercomplex, exhibiting a variety of conformations, have uncovered the dual functions of M1249L. During early transcription, M1249L could serve as multiple temporary transcription factors with C-terminal domain acting as a switcher for activation/inactivation, while during late transcription it aids in the packaging of the transcription machinery. The structural and functional characteristics of M1249L underscore its vital roles in ASFV transcription, packaging, and capsid assembly, presenting novel opportunities for therapeutic intervention.
History
DepositionMar 20, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39529.png

Downloads & links

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Map

FileDownload / File: emd_39529.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 320 pix.
= 258.56 Å		0.81 Å/pix.
x 320 pix.
= 258.56 Å		0.81 Å/pix.
x 320 pix.
= 258.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0098
Minimum - Maximum-0.03858698 - 0.053377695
Average (Standard dev.)0.0000802372 (±0.003041854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 258.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39529_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_39529_half_map_2.map
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Sample components

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Entire : African swine fever virus RNA polymerase complex

EntireName: African swine fever virus RNA polymerase complex
Components
  • Complex: African swine fever virus RNA polymerase complex

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Supramolecule #1: African swine fever virus RNA polymerase complex

SupramoleculeName: African swine fever virus RNA polymerase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: African swine fever virus

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / 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: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9630
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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