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- EMDB-39522: ASFV RNA polymerase-M1249L complex 15 -

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Basic information

Entry
Database: EMDB / ID: EMD-39522
TitleASFV RNA polymerase-M1249L complex 15
Map data
Sample
  • Complex: ASFV RNA polymerase-M1249L complex 6
KeywordsASFV / vRNAP / VIRAL PROTEIN
Biological speciesAfrican swine fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.53 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_39522.png

Downloads & links

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Map

FileDownload / File: emd_39522.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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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: 0.009
Minimum - Maximum-0.02207394 - 0.0327244
Average (Standard dev.)0.0000065710788 (±0.0024308641)
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_39522_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_39522_half_map_2.map
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Sample components

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Entire : ASFV RNA polymerase-M1249L complex 6

EntireName: ASFV RNA polymerase-M1249L complex 6
Components
  • Complex: ASFV RNA polymerase-M1249L complex 6

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Supramolecule #1: ASFV RNA polymerase-M1249L complex 6

SupramoleculeName: ASFV RNA polymerase-M1249L complex 6 / type: complex / ID: 1 / Parent: 0
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

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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: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5609
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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