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Open data
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Basic information
Entry | Database: PDB / ID: 6o6b | ||||||||||||
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Title | Rotavirus A-VP3 (RVA-VP3) | ||||||||||||
![]() | Protein VP3 | ||||||||||||
![]() | STRUCTURAL PROTEIN / Rotavirus / Capping enzyme / Methyl transferase / RTPase / PDE | ||||||||||||
Function / homology | ![]() Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / hydrolase activity / virus-mediated perturbation of host defense response / GTP binding / RNA binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
![]() | Kumar, D. / Yu, X. / Prasad, V. / Wang, Z. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 592.9 KB | Display | ![]() |
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PDB format | ![]() | 466 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 94.8 KB | Display | |
Data in CIF | ![]() | 138.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0632MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 97703.820 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q1WK45, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases, mRNA guanylyltransferase, mRNA (guanine-N7)-methyltransferase #2: Chemical | ChemComp-5GP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: VP3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: PRION |
Buffer solution | pH: 7 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 recording | Average 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 scans | Width: 7420 / Height: 7676 / Movie frames/image: 50 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 133712 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D2 (2x2 fold dihedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70892 / Symmetry type: POINT |