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- PDB-9i7w: Extended and wrapped protein P7 dimers of dimers, the P1 layer an... -

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Basic information

Entry
Database: PDB / ID: 9i7w
TitleExtended and wrapped protein P7 dimers of dimers, the P1 layer and the RNA-dependent RNA polymerase P2 in transcribing particles of bacteriophage phi6
Components
  • DNA (5'-D(*TP*TP*TP*CP*C)-3')
  • Major inner protein P1
  • Nucleocapsid protein
  • RNA-directed RNA polymerase
KeywordsVIRAL PROTEIN / inner protein capsid / transcribing phi6 particle / localized reconstruction
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
DNA / RNA-directed RNA polymerase / Major inner protein P1 / Nucleocapsid protein
Similarity search - Component
Biological speciesCystovirus phi6
synthetic construct (others)
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
DepositionFeb 3, 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

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Assembly

Deposited unit
x: DNA (5'-D(*TP*TP*TP*CP*C)-3')
U: RNA-directed RNA polymerase
A: Nucleocapsid protein
B: Nucleocapsid protein
E: Nucleocapsid protein
F: Nucleocapsid protein
M: Nucleocapsid protein
N: Nucleocapsid protein
S: Nucleocapsid protein
T: Nucleocapsid protein
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)511,62614
Polymers511,62614
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: DNA chain DNA (5'-D(*TP*TP*TP*CP*C)-3')


Mass: 1445.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein RNA-directed RNA polymerase / Protein P2


Mass: 74903.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cystovirus phi6 / References: UniProt: P11124, RNA-directed RNA polymerase
#3: Protein
Nucleocapsid protein / Procapsid assembly protein / p7


Mass: 12017.965 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Cystovirus phi6 / References: UniProt: Q283U0
#4: Protein
Major inner protein P1


Mass: 84783.359 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 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: 42 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: UCSF ChimeraX / Category: model fitting
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 buildingProtocol: RIGID BODY FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11HHT

1hht

11HHT1PDBexperimental model
29HTW

9htw

19HTW2PDBexperimental model
39I5C

9i5c

19I5C3PDBexperimental model

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