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- PDB-8b4z: Rosellinia necatrix megabirnavirus 1-W779 full capsid -

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Basic information

Entry
Database: PDB / ID: 8b4z
TitleRosellinia necatrix megabirnavirus 1-W779 full capsid
ComponentsMajor capsid protein A
KeywordsVIRUS / viruses / dsRNA / capsid / cryo-EM / fungus / Megabirnaviridae / mycoviruses
Function / homologyCoat protein
Function and homology information
Biological speciesRosellinia necatrix megabirnavirus 1/W779
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWang, H. / Okamoto, K. / Miyazaki, N. / Suzuki, N.
Funding support Sweden, Japan, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: PLoS Pathog / Year: 2023
Title: Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture.
Authors: Han Wang / Lakha Salaipeth / Naoyuki Miyazaki / Nobuhiro Suzuki / Kenta Okamoto /
Abstract: Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces ...Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Compared with other non-enveloped icosahedral dsRNA viruses, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus.
History
DepositionSep 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein A
B: Major capsid protein A


Theoretical massNumber of molelcules
Total (without water)272,1702
Polymers272,1702
Non-polymers00
Water00
1
A: Major capsid protein A
B: Major capsid protein A
x 60


Theoretical massNumber of molelcules
Total (without water)16,330,194120
Polymers16,330,194120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Major capsid protein A


Mass: 136084.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rosellinia necatrix megabirnavirus 1/W779 / Strain: isolate -/Japan/W779/2001 / References: UniProt: D0FZL0

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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: Rosellinia necatrix megabirnavirus 1/W779 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Rosellinia necatrix megabirnavirus 1/W779
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2750 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12230 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00719100
ELECTRON MICROSCOPYf_angle_d0.63725916
ELECTRON MICROSCOPYf_dihedral_angle_d17.4722667
ELECTRON MICROSCOPYf_chiral_restr0.0482816
ELECTRON MICROSCOPYf_plane_restr0.0043437

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