|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|
|Function / homology||Rubella membrane glycoprotein E2 / Rubella capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1 / T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell ...Rubella membrane glycoprotein E2 / Rubella capsid protein / Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1 / T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral nucleocapsid / viral envelope / virion attachment to host cell / virion membrane / RNA binding / integral component of membrane / Structural polyprotein|
Function and homology information
|Specimen source||Rubella virus / / virus|
|Method||ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 11.1 Å resolution|
|Authors||Mangala Prasad, V. / Klose, T. / Rossmann, M.G.|
|Citation||Journal: PLoS Pathog. / Year: 2017|
Title: Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus.
Authors: Vidya Mangala Prasad / Thomas Klose / Michael G Rossmann
Abstract: Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe ...Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway.
SummaryFull reportAbout validation report
|Date||Deposition: Jun 14, 2016 / Release: May 10, 2017|
|Structure viewer||Molecule: |
Downloads & links
A: E1 glycoprotein
|#1: Protein/peptide|| |
Mass: 50573.352 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 583-1018) / Source: (gene. exp.) Rubella virus / / virus / Production host: Cercopithecus aethiops / 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 FIELDBright-field microscopy / 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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