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- PDB-6o6b: Rotavirus A-VP3 (RVA-VP3) -

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Basic information

Entry
Database: PDB / ID: 6o6b
TitleRotavirus A-VP3 (RVA-VP3)
ComponentsProtein VP3
KeywordsSTRUCTURAL PROTEIN / Rotavirus / Capping enzyme / Methyl transferase / RTPase / PDE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / viral process / viral nucleocapsid / mRNA guanylyltransferase / mRNA guanylyltransferase activity / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / symbiont-mediated suppression of host innate immune response / hydrolase activity / GTP binding / RNA binding
Similarity search - Function
Protein VP3, rotavirus / Rotavirus VP3 protein / Viral protein 3 containing mRNA (guanine-N(7)-)-methyltransferase family profile.
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Protein VP3
Similarity search - Component
Biological speciesRotavirus A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKumar, D. / Yu, X. / Prasad, V. / Wang, Z.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 United States
Welch FoundationQ-1967-20180324 United States
Robert A. Welch FoundationQ1279 United States
CitationJournal: To Be Published
Title: A sub-atomic resolution cryo-EM of full-length Rotavirus A-VP3 (RVA-VP3)
Authors: Kumar, D. / Yu, X. / Prasad, V. / Wang, Z.
History
DepositionMar 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Mar 11, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2020Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2020Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Jul 1, 2026Group: Atomic model / Data collection / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _em_admin.last_update
Revision 1.1Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Protein VP3
B: Protein VP3
C: Protein VP3
D: Protein VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,2688
Polymers390,8154
Non-polymers1,4534
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration profile indicates a tetrameric assembly in solution, equilibrium centrifugation, Analytical Ultracentrifugation confirms tetrameric state is preferred ...Evidence: gel filtration, Gel filtration profile indicates a tetrameric assembly in solution, equilibrium centrifugation, Analytical Ultracentrifugation confirms tetrameric state is preferred oligomeric assembly in solution
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19750 Å2
ΔGint-95 kcal/mol
Surface area134020 Å2

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Components

#1: Protein
Protein VP3


Mass: 97703.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Gene: VP3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q1WK45, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, mRNA guanylyltransferase, mRNA (guanine-N7)-methyltransferase
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
Has protein modificationN

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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: VP3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rotavirus A
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: PRION
Buffer solutionpH: 7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 4.7 mm / C2 aperture diameter: 100 µm
Image recordingAverage exposure time: 10 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 7420 / Height: 7676 / Movie frames/image: 50

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1EMAN22.2particle selectionEMAN2 e2boxer.py was uesed to automatically select particle images
2SerialEM3.6image acquisition
4Gctf1.06CTF correction
10RELION2.1.0initial Euler assignment
11RELION2.1.0final Euler assignment
12RELION2.1.0classification
13RELION2.1.03D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 133712
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70892 / Symmetry type: POINT

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