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- PDB-9i5c: Inner layer protein P1 chains in transcribing particles of bacter... -

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Basic information

Entry
Database: PDB / ID: 9i5c
TitleInner layer protein P1 chains in transcribing particles of bacteriophage phi6
ComponentsMajor inner protein P1
KeywordsVIRAL PROTEIN / structural protein / inner protein layer / transcribing particle
Function / homology: / Major inner capsid protein P1 / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1
Function and homology information
Biological speciesCystovirus phi6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsKumpula, E.-P. / Ilca, S.L. / 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
DepositionJan 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: Major inner protein P1
W: Major inner protein P1
X: Major inner protein P1
Z: Major inner protein P1


Theoretical massNumber of molelcules
Total (without water)340,3234
Polymers340,3234
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: 85080.711 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cystovirus phi6 / References: UniProt: P11126
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 shellName: Outer protein shell / Triangulation number (T number): 13
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: 42 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
7ISOLDEmodel fitting
9PHENIX1.21.2_5419model refinement10.1107/S2059798319011471
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18230 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6HY0

6hy0


Accession code: 6HY0 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 101.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005924340
ELECTRON MICROSCOPYf_angle_d0.855233076
ELECTRON MICROSCOPYf_chiral_restr0.0473792
ELECTRON MICROSCOPYf_plane_restr0.01154284
ELECTRON MICROSCOPYf_dihedral_angle_d15.18348872

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