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- PDB-9hu5: Asymmetric unit from transcribing single-layered particle of bact... -

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Basic information

Entry
Database: PDB / ID: 9hu5
TitleAsymmetric unit from transcribing single-layered particle of bacteriophage phi6
Components
  • Major inner protein P1
  • NTPase
KeywordsVIRUS / cystovirus / phi6 / semi-conservative transcription / cryo-EM / cryogenic electron microscopy / localized reconstruction / symmetry relaxation / dsRNA virus / bacteriophage
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral genome packaging / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding
Similarity search - Function
: / Major inner capsid protein P1 / Packaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Major inner protein P1 / NTPase
Similarity search - Component
Biological speciesCystovirus phi6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsIlca, S.L. / Kumpula, E.-P. / Huiskonen, J.T.
Funding support Finland, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
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Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
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Revision 1.1Jan 21, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major inner protein P1
B: Major inner protein P1
C: NTPase


Theoretical massNumber of molelcules
Total (without water)173,7013
Polymers173,7013
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Major inner protein P1


Mass: 84783.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cystovirus phi6 / References: UniProt: P11126
#2: Protein/peptide NTPase / Nucleocapsid protein / p4


Mass: 4134.507 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cystovirus phi6 / References: UniProt: Q283T8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cystovirus phi6 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cystovirus phi6
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Virus shell
IDEntity assembly-IDNameTriangulation number (T number)
11Outer protein shell13
21Inner protein shell1
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 41000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 391662 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.93 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003212315
ELECTRON MICROSCOPYf_angle_d0.749116730
ELECTRON MICROSCOPYf_chiral_restr0.04571916
ELECTRON MICROSCOPYf_plane_restr0.00992167
ELECTRON MICROSCOPYf_dihedral_angle_d14.26934491

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