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- PDB-9rch: Cryo-EM structure of Yadonushi Virus 1 -

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Basic information

Entry
Database: PDB / ID: 9rch
TitleCryo-EM structure of Yadonushi Virus 1
Components(Coat protein) x 2
KeywordsVIRUS / CryoEM / Virion / Yadokari / Mycovirus
Function / homologyE3 ligase, CCCH-type zinc finger / CCCH-type zinc finger / Zinc finger, CCCH-type superfamily / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / viral capsid / zinc ion binding / Coat protein
Function and homology information
Biological speciesRosellinia necatrix (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsNovoa, G. / Suzuki, N. / Caston, J.R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-146143NB-I00 Spain
CitationJournal: To Be Published
Title: Cryo-EM structure of Yadonushi Virus 1 at 2.2 Angstroms resolution
Authors: Novoa, G. / Suzuki, N. / Caston, J.R.
History
DepositionMay 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 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: Coat protein
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)226,8962
Polymers226,8962
Non-polymers00
Water00
1
A: Coat protein
B: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)13,613,775120
Polymers13,613,775120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Coat protein


Mass: 111298.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rosellinia necatrix (fungus) / References: UniProt: A0A2Z5Q2Q8
#2: Protein Coat protein


Mass: 115597.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rosellinia necatrix (fungus) / References: UniProt: A0A2Z5Q2Q8
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: Yadonushi Virus 1 / Type: VIRUS
Details: R. necatrix strain W1032 contains different type of Yadonushi Virus 1: strain A, B and C.
Entity ID: all / Source: NATURAL
Source (natural)Organism: Yadonushi Virus 1 / Strain: A, B, C
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Rosellinia necatrix / Strain: W1032
Virus shellDiameter: 540 nm / Triangulation number (T number): 1
Buffer solutionpH: 7 / Details: Phosphate buffer 0.05M
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: 2300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.1_3865 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 550000 / Symmetry type: POINT

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