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- PDB-5mm2: nora virus structure -

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Basic information

Entry
Database: PDB / ID: 5mm2
Titlenora virus structure
Components
  • Capsid protein VP4A
  • capsid protein VP4B
  • capsid protein VP4C
KeywordsVIRUS / nora virus / cryo-em / single particle analysis / capsid
Function / homologyviral capsid / Capsid protein / ORF4 polyprotein
Function and homology information
Biological speciesNora virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLaurinmaki, P. / Shakeel, S. / Ekstrom, J.-O. / Butcher, S.J.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland139178 Finland
Academy of Finland275199 Finland
Sigrid Juselius Foundation Finland
CitationJournal: Sci Rep / Year: 2020
Title: Structure of Nora virus at 2.7 Å resolution and implications for receptor binding, capsid stability and taxonomy.
Authors: Pasi Laurinmäki / Shabih Shakeel / Jens-Ola Ekström / Pezhman Mohammadi / Dan Hultmark / Sarah J Butcher /
Abstract: Nora virus, a virus of Drosophila, encapsidates one of the largest single-stranded RNA virus genomes known. Its taxonomic affinity is uncertain as it has a picornavirus-like cassette of enzymes for ...Nora virus, a virus of Drosophila, encapsidates one of the largest single-stranded RNA virus genomes known. Its taxonomic affinity is uncertain as it has a picornavirus-like cassette of enzymes for virus replication, but the capsid structure was at the time for genome publication unknown. By solving the structure of the virus, and through sequence comparison, we clear up this taxonomic ambiguity in the invertebrate RNA virosphere. Despite the lack of detectable similarity in the amino acid sequences, the 2.7 Å resolution cryoEM map showed Nora virus to have T = 1 symmetry with the characteristic capsid protein β-barrels found in all the viruses in the Picornavirales order. Strikingly, α-helical bundles formed from the extended C-termini of capsid protein VP4B and VP4C protrude from the capsid surface. They are similar to signalling molecule folds and implicated in virus entry. Unlike other viruses of Picornavirales, no intra-pentamer stabilizing annulus was seen, instead the intra-pentamer stability comes from the interaction of VP4C and VP4B N-termini. Finally, intertwining of the N-termini of two-fold symmetry-related VP4A capsid proteins and RNA, provides inter-pentamer stability. Based on its distinct structural elements and the genetic distance to other picorna-like viruses we propose that Nora virus, and a small group of related viruses, should have its own family within the order Picornavirales.
History
DepositionDec 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.2Feb 10, 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 1.3May 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_assembly / pdbx_struct_assembly_gen / 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_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

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Assembly

Deposited unit
A: capsid protein VP4C
B: capsid protein VP4B
C: Capsid protein VP4A


Theoretical massNumber of molelcules
Total (without water)102,4453
Polymers102,4453
Non-polymers00
Water00
1
A: capsid protein VP4C
B: capsid protein VP4B
C: Capsid protein VP4A
x 60


Theoretical massNumber of molelcules
Total (without water)6,146,695180
Polymers6,146,695180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation59
Buried area8290 Å2
ΔGint-17 kcal/mol
Surface area40730 Å2
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein capsid protein VP4C


Mass: 45258.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nora virus / References: UniProt: Q27YG7
#2: Protein capsid protein VP4B


Mass: 28166.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nora virus / References: UniProt: Q27YG7
#3: Protein Capsid protein VP4A


Mass: 29019.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nora virus / References: UniProt: D2WFA0

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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: Nora virus / Type: VIRUS
Details: Drosophila Nora virus strain Umea 2007 was derived from an infectious cDNA clone (accession GQ257737).
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Nora virus
Source (recombinant)Organism: Drosophila (fruit flies) / Plasmid: pRmHa-3
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Drosophila melanogaster
Virus shellTriangulation number (T number): 1
Buffer solutionpH: 7.4 / Details: 10mM Tris-HCl pH 7.4.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 295 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 / Calibrated magnification: 47170 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3516
EM imaging opticsEnergyfilter name: GIF Quantum
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategory
1ETHAN1.2particle selection
2EPUimage acquisition
4CTFFIND4.0.16CTF correction
7Coot0.8.1model fitting
9Coot0.8.1model refinement
10PHENIXdev-2067-000model refinement
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
13RELION1.4classification
14RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 30313
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16131 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient

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