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- PDB-5nd1: Viral evolution results in multiple, surface-allocated enzymatic ... -

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Entry
Database: PDB / ID: 5nd1
TitleViral evolution results in multiple, surface-allocated enzymatic activities in a fungal double-stranded RNA virus
Components(Capsid proteinCapsid) x 2
KeywordsVIRUS / RnQV1 / dsRNA virus / fungal virus
Function / homologyCapsid protein / Capsid protein
Function and homology information
Biological speciesRosellinia necatrix quadrivirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMata, C.P. / Luque, D. / Gomez Blanco, J. / Rodriguez, J.M. / Suzuki, N. / Ghabrial, S.A. / Carrascosa, J.L. / Trus, B.L. / Caston, J.R.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-55475-R Spain
Comunidad Autonoma de MadridS2013/MIT-2807 Spain
CitationJournal: PLoS Pathog / Year: 2017
Title: Acquisition of functions on the outer capsid surface during evolution of double-stranded RNA fungal viruses.
Authors: Carlos P Mata / Daniel Luque / Josué Gómez-Blanco / Javier M Rodríguez / José M González / Nobuhiro Suzuki / Said A Ghabrial / José L Carrascosa / Benes L Trus / José R Castón /
Abstract: Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3. ...Unlike their counterparts in bacterial and higher eukaryotic hosts, most fungal viruses are transmitted intracellularly and lack an extracellular phase. Here we determined the cryo-EM structure at 3.7 Å resolution of Rosellinia necatrix quadrivirus 1 (RnQV1), a fungal double-stranded (ds)RNA virus. RnQV1, the type species of the family Quadriviridae, has a multipartite genome consisting of four monocistronic segments. Whereas most dsRNA virus capsids are based on dimers of a single protein, the ~450-Å-diameter, T = 1 RnQV1 capsid is built of P2 and P4 protein heterodimers, each with more than 1000 residues. Despite a lack of sequence similarity between the two proteins, they have a similar α-helical domain, the structural signature shared with the lineage of the dsRNA bluetongue virus-like viruses. Domain insertions in P2 and P4 preferential sites provide additional functions at the capsid outer surface, probably related to enzyme activity. The P2 insertion has a fold similar to that of gelsolin and profilin, two actin-binding proteins with a function in cytoskeleton metabolism, whereas the P4 insertion suggests protease activity involved in cleavage of the P2 383-residue C-terminal region, absent in the mature viral particle. Our results indicate that the intimate virus-fungus partnership has altered the capsid genome-protective and/or receptor-binding functions. Fungal virus evolution has tended to allocate enzyme activities to the virus capsid outer surface.
History
DepositionMar 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.2Oct 24, 2018Group: Data collection / 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
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)261,2222
Polymers261,2222
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint-85 kcal/mol
Surface area68510 Å2
MethodPISA

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Components

#1: Protein Capsid protein / Capsid


Mass: 147782.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rosellinia necatrix quadrivirus 1 / References: UniProt: M1VMJ0
#2: Protein Capsid protein / Capsid


Mass: 113439.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rosellinia necatrix quadrivirus 1 / References: UniProt: M1VHN2

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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: virus / Type: VIRUS / Entity ID: all
Molecular weightValue: 15.9 MDa / Experimental value: YES
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Rosellinia necatrix
Virus shellName: P2 and P4 capsid proteins / Diameter: 470 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.8 / Details: 50 mM 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: LEICA EM CPC / Cryogen 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 FIELDBright-field microscopy / Calibrated defocus min: 700 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 1.7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 24 / Used frames/image: 4-21

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Processing

EM software
IDNameVersionCategory
1Xmipp3particle selection
4CTFFIND3CTF correction
7Cootmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13Cootmodel refinement
14REFMAC5model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 53683
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37531 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE

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