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- PDB-7d0l: The major capsid of Omono River virus (strain:LZ), protrusion-fre... -

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Basic information

Entry
Database: PDB / ID: 7d0l
TitleThe major capsid of Omono River virus (strain:LZ), protrusion-free status.
ComponentsCapsid protein
KeywordsVIRUS / Totiviridae / major capsid / viral protein
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 / Main capsid protein
Function and homology information
Biological speciesOmono River virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsShao, Q. / Jia, X. / Gao, Y. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570736 China
CitationJournal: PLoS Pathog / Year: 2021
Title: Cryo-EM reveals a previously unrecognized structural protein of a dsRNA virus implicated in its extracellular transmission.
Authors: Qianqian Shao / Xudong Jia / Yuanzhu Gao / Zhe Liu / Huan Zhang / Qiqi Tan / Xin Zhang / Huiqiong Zhou / Yinyin Li / De Wu / Qinfen Zhang /
Abstract: Mosquito viruses cause unpredictable outbreaks of disease. Recently, several unassigned viruses isolated from mosquitoes, including the Omono River virus (OmRV), were identified as totivirus-like ...Mosquito viruses cause unpredictable outbreaks of disease. Recently, several unassigned viruses isolated from mosquitoes, including the Omono River virus (OmRV), were identified as totivirus-like viruses, with features similar to those of the Totiviridae family. Most reported members of this family infect fungi or protozoans and lack an extracellular life cycle stage. Here, we identified a new strain of OmRV and determined high-resolution structures for this virus using single-particle cryo-electron microscopy. The structures feature an unexpected protrusion at the five-fold vertex of the capsid. Disassociation of the protrusion could result in several conformational changes in the major capsid. All these structures, together with some biological results, suggest the protrusions' associations with the extracellular transmission of OmRV.
History
DepositionSep 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: 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 1.2Mar 27, 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 / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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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)193,7222
Polymers193,7222
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,623,319120
Polymers11,623,319120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area8830 Å2
ΔGint-36 kcal/mol
Surface area59550 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
x 5


  • icosahedral pentamer
  • 969 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)968,61010
Polymers968,61010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 1.16 MDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)1,162,33212
Polymers1,162,33212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein


Mass: 96860.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Omono River virus / Cell line: C6/36 / Strain: LZ / References: UniProt: A0A7M3VBX7*PLUS

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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: Major capsid dimer of OmRV-LZ (protrusion-free status)
Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Omono River virus / Strain: LZ
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Culex quinquefasciatus
Virus shellName: Major capsid / Diameter: 450 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1136.89 mMsodium chorideNaCl1
22.67 mMpotassium chlorideKCl1
38.1 mMdisodium hydrogen phosphateNa2HPO41
41.76 mMpotassium dihydrogen phosphateKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Alignment procedure: NONE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 39 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2ETHANparticle selection
3EPUimage acquisition
5GctfCTF correction
10PHENIX1.17model refinement
11RELIONinitial Euler assignment
12jsprfinal Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 96668
Details: Subtracted from every five-fold vertexes from 96668 virus particles. Each virus contains 12 five-fold vertexes. 96668x12=1160016.
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15240 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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