|Entry||Database: PDB / ID: 5khc|
|Title||Structure of rubella virus E1 glycoprotein ectodomain fitted into sub-tomogram averaged surface spike density of rubella virus|
|Keywords||VIRAL PROTEIN / Rubella virus / surface glycoprotein spike / E1-E2 heterodimer|
|Specimen source||Rubella virus / virus / RUBV / 風疹ウイルス|
|Method||Electron microscopy (11.1 Å resolution / Particle / Subtomogram averaging)|
|Authors||Mangala Prasad, V. / Klose, T. / Rossmann, M.G.|
|Citation||PLoS Pathog., 2017, 13, e1006377-e1006377|
SummaryFull reportAbout validation report
|Date||Deposition: Jun 14, 2016 / Release: May 10, 2017|
Downloads & links
A: E1 glycoprotein
Mass: 50573.352 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 583-1018)
Source: (gene. exp.) Rubella virus / virus / 風疹ウイルス
References: UniProt: P08563
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SUBTOMOGRAM AVERAGING|
|Component||Name: Rubella virus E1-E2 glycoprotein spike / Type: COMPLEX / Entity ID: 1 / Source: MULTIPLE SOURCES|
|Molecular weight||Value: 0.085 deg. / Units: MEGADALTONS / Experimental value: NO|
|Buffer solution||pH: 8|
|Specimen||Conc.: 1 mg/ml|
Details: Rubella virus was purified from Vero cells. Glycoprotein spike volumes were extracted from the surface of virus tomograms.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
|Specimen support||Grid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R 1.2/1.3|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 11000 / Nominal defocus max: 500 nm / Nominal defocus min: 400 nm|
|Image recording||Electron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7290 / Symmetry type: POINT|
|EM volume selection||Method: manual picking / Number of tomograms: 15 / Number of volumes extracted: 7500|
|Atomic model building||Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf|
|Atomic model building||PDB-ID: 4ADG|
Pdb chain ID: A / Pdb chain residue range: 1-421
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