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- PDB-9rvm: Penicillium chrysogenum Virus full virions -

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Basic information

Entry
Database: PDB / ID: 9rvm
TitlePenicillium chrysogenum Virus full virions
Components
  • Capsid protein
  • Protein 4 Penicillium chrysogenum Virus
KeywordsVIRUS / Cryo-EM / PcV / Virus.
Function / homology: / : / Fungal virus Capsid protein, N-terminal domain / Fungal virus Capsid protein, C-terminal domain / T=1 icosahedral viral capsid / Uncharacterized protein p4 / Capsid protein
Function and homology information
Biological speciesPenicillium chrysogenum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsGil-Cantero, D. / Novoa Benavides, G. / Luque, D. / Ruiz Caston, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2023-146143NB-I00 Spain
CitationJournal: To Be Published
Title: Penicillium chrysogenum Virus full virions
Authors: Gil-Cantero, D. / Novoa Benavides, G. / Luque, D. / Ruiz Caston, J.
History
DepositionJul 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 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

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Assembly

Deposited unit
A: Capsid protein
B: Protein 4 Penicillium chrysogenum Virus


Theoretical massNumber of molelcules
Total (without water)122,4152
Polymers122,4152
Non-polymers00
Water00
1
A: Capsid protein
B: Protein 4 Penicillium chrysogenum Virus
x 60


Theoretical massNumber of molelcules
Total (without water)7,344,918120
Polymers7,344,918120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Capsid protein / CP / Coat protein


Mass: 60430.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium chrysogenum (fungus) / References: UniProt: Q8JVC1
#2: Protein Protein 4 Penicillium chrysogenum Virus


Mass: 61985.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium chrysogenum (fungus) / References: UniProt: Q8JVB9
Has protein modificationY

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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: Penicillium chrysogenum virus (isolate Caston) / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 120 kDa/nm / Experimental value: YES
Source (natural)Organism: Penicillium chrysogenum virus (isolate Caston)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Penicillium chrysogenum virus (isolate Caston)
Buffer solutionpH: 7.8 / Details: 50mM Tris-HCl pH 7.8; 150 mM NaCl; 5 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 22 K
Details: 3 min incubation in carbon covered grids R2/2 Cu/Rh. Blotted 3 s at force 0

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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 magnification: 83000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameCategory
1Xmippparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2244540
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1269168 / Symmetry type: POINT

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