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- EMDB-52389: Localized reconstruction of polymerase P2 from transcribing singl... -

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Basic information

Entry
Database: EMDB / ID: EMD-52389
TitleLocalized reconstruction of polymerase P2 from transcribing single-layered particle of bacteriophage phi6 in stage B
Map data
Sample
  • Virus: Cystovirus phi6
Keywordscystovirus / phi6 / semi-conservative transcription / cryo-EM / cryogenic electron microscopy / localized reconstruction / symmetry relaxation / virus / dsRNA virus / bacteriophage
Function / homology
Function and homology information


RNA uridylyltransferase activity / T=2 icosahedral viral capsid / viral inner capsid / virion component / viral nucleocapsid / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription ...RNA uridylyltransferase activity / T=2 icosahedral viral capsid / viral inner capsid / virion component / viral nucleocapsid / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding / metal ion binding / identical protein binding
Similarity search - Function
: / Major inner capsid protein P1 / Cystovirus, RNA-directed RNA polymerase, N-terminal / Cystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase / Major inner protein P1 / Nucleocapsid protein
Similarity search - Component
Biological speciesCystovirus phi6
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsIlca SL / Huiskonen JT
Funding support Finland, 1 items
OrganizationGrant numberCountry
Academy of Finland331627 Finland
CitationJournal: Mol Cell / Year: 2026
Title: Capsid restructuring activates semi-conservative dsRNA transcription in cystovirus ɸ6.
Authors: Serban L Ilca / Xiaoyu Sun / Esa-Pekka Kumpula / Katri Eskelin / David I Stuart / Minna M Poranen / Juha T Huiskonen /
Abstract: Double-stranded (ds)RNA viruses replicate and transcribe their genome within a proteinaceous viral capsid to evade host cell defenses. While Reovirales members use conservative transcription, most ...Double-stranded (ds)RNA viruses replicate and transcribe their genome within a proteinaceous viral capsid to evade host cell defenses. While Reovirales members use conservative transcription, most dsRNA viruses, including cystoviruses, utilize semi-conservative transcription, in which a newly synthesized positive strand replaces the parental positive strand, which is released as mRNA. Here, we visualize semi-conservative transcription activation in cystovirus ɸ6 double-layered particles using cryogenic electron microscopy. We observe nucleotide-triggered disassembly of the domain-swapped outer capsid layer, subsequent expansion of the inner capsid layer, and stepwise assembly of transcription complexes at the opposing poles of the spooled dsRNA genome. These complexes consist of the viral polymerases embedded into a triskelion formed by the minor protein P7, which we show as essential for continuous transcription. The packaging hexamers proximal to the transcription sites channel the viral mRNA exit. Our results define the complex molecular pathway from the quiescent state to activated semi-conservative transcription.
History
DepositionDec 20, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52389.png

Downloads & links

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Map

FileDownload / File: emd_52389.map.gz / Format: CCP4 / Size: 27 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.)
1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å		1.4 Å/pix.
x 192 pix.
= 268.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.104867704 - 0.17045307
Average (Standard dev.)0.00011375927 (±0.018600885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52389_msk_1.map
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Additional map: #1

Fileemd_52389_additional_1.map
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Half map: #1

Fileemd_52389_half_map_1.map
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Half map: #2

Fileemd_52389_half_map_2.map
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Sample components

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Entire : Cystovirus phi6

EntireName: Cystovirus phi6
Components
  • Virus: Cystovirus phi6

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Supramolecule #1: Cystovirus phi6

SupramoleculeName: Cystovirus phi6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / NCBI-ID: 10879 / Sci species name: Cystovirus phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Name: Outer protein shell / T number (triangulation number): 13
Virus shellShell ID: 2 / Name: Inner protein shell / T number (triangulation number): 1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 41.0 µm / Nominal defocus min: 2.0 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: EMDB MAP
EMDB ID:

0299

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 18230
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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