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- PDB-9hu4: Asymmetric unit from transcribing double-layered particle of bact... -

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Basic information

Entry
Database: PDB / ID: 9hu4
TitleAsymmetric unit from transcribing double-layered particle of bacteriophage phi6
Components
  • Major inner protein P1
  • Major outer capsid protein
  • 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=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral genome packaging / viral inner capsid / viral outer 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 outer capsid protein / Major inner protein P1 / NTPase
Similarity search - Component
Biological speciesCystovirus phi6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsIlca, S.L. / Huiskonen, J.T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland331627 Finland
CitationJournal: To be published
Title: Restructuring of bacteriophage phi6 viral particle activates semi-conservative transcription
Authors: Ilca, S.L. / Sun, X. / Kumpula, E.-P. / Eskelin, K. / Poranen, M.M. / Huiskonen, J.T.
History
DepositionDec 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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
D: Major outer capsid protein
E: Major outer capsid protein
F: Major outer capsid protein
G: Major outer capsid protein
H: Major outer capsid protein
I: Major outer capsid protein
J: Major outer capsid protein
K: Major outer capsid protein
L: Major outer capsid protein
M: Major outer capsid protein


Theoretical massNumber of molelcules
Total (without water)333,01513
Polymers333,01513
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
#3: Protein
Major outer capsid protein / Protein P8


Mass: 15931.340 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Cystovirus phi6 / References: UniProt: P07579
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: FEI TITAN 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 software
IDNameCategory
9PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2504986 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00823803
ELECTRON MICROSCOPYf_angle_d0.73132304
ELECTRON MICROSCOPYf_dihedral_angle_d7.48314503
ELECTRON MICROSCOPYf_chiral_restr0.0463741
ELECTRON MICROSCOPYf_plane_restr0.0054206

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