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- PDB-6s2c: Acquired functional capsid structures in metazoan totivirus-like ... -

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Entry
Database: PDB / ID: 6s2c
TitleAcquired functional capsid structures in metazoan totivirus-like dsRNA virus.
Components(Capsid protein) x 2
KeywordsVIRUS / Mosquito / Totivirus / Totiviridae / Totivirus-like virus / dsRNA / capsid
Function / homologyDouble-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / RNA binding / Capsid protein
Function and homology information
Biological speciesOmono River virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsOkamoto, K. / Larsson, S.D.D. / Maia, R.N.C.F. / Murata, K. / Hajdu, J. / Iwasaki, K. / Miyazaki, N.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Swedish Research Council2018-00421 Sweden
Swedish Research CouncilJA2014-5721 Sweden
CitationJournal: Structure / Year: 2020
Title: Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus.
Authors: Kenta Okamoto / Ricardo J Ferreira / Daniel S D Larsson / Filipe R N C Maia / Haruhiko Isawa / Kyoko Sawabe / Kazuyoshi Murata / Janos Hajdu / Kenji Iwasaki / Peter M Kasson / Naoyuki Miyazaki /
Abstract: Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid ...Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid structure, which suffices for the intracellular phase in their life cycle, metazoan dsRNA viruses have acquired additional structural features as an adaptation for extracellular cell-to-cell transmission in multicellular hosts. Here, we present the first atomic model of a metazoan dsRNA totivirus-like virus and the structure reveals three unique structural traits: a C-terminal interlocking arm, surface projecting loops, and an obstruction at the pore on the 5-fold symmetry axis. These traits are keys to understanding the capsid functions of metazoan dsRNA viruses, such as particle stability and formation, cell entry, and endogenous intraparticle transcription of mRNA. On the basis of molecular dynamics simulations of the obstructed pore, we propose a possible mechanism of intraparticle transcription in totivirus-like viruses, which dynamically switches between open and closed states of the pore(s).
History
DepositionJun 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)182,6402
Polymers182,6402
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)10,958,381120
Polymers10,958,381120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Capsid protein


Mass: 91202.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Omono River virus / References: UniProt: E1CI69
#2: Protein Capsid protein


Mass: 91436.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Omono River virus / References: UniProt: E1CI69

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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: Omono River virus / Type: VIRUS
Details: Omono River virus particles from C6/36 mosquito cells
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Omono River virus / Strain: AK4
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Aedes
Virus shellName: Capsid / Diameter: 420 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.5
Buffer componentConc.: 100 mM / Name: ammonium acetate / Formula: C2H7NO2
SpecimenConc.: 1.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 59000 X / Nominal defocus max: 225 nm / Nominal defocus min: 100 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 4521
Image scansMovie frames/image: 16

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
4CTFFIND4CTF correction
7Coot0.8.9model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13jspr3D reconstruction
14PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 30986
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30363 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient

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