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- PDB-5khc: Structure of rubella virus E1 glycoprotein ectodomain fitted into... -

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Basic information

Entry
Database: PDB / ID: 5khc
TitleStructure of rubella virus E1 glycoprotein ectodomain fitted into sub-tomogram averaged surface spike density of rubella virus
ComponentsE1 glycoprotein
KeywordsVIRAL PROTEIN / Rubella virus / surface glycoprotein spike / E1-E2 heterodimer
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / membrane / metal ion binding
Similarity search - Function
Rubella capsid / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella membrane glycoprotein E1, domain 2 / Rubella membrane glycoprotein E1, domain 3 / Rubella membrane glycoprotein E1, domain 1 / Rubella capsid domain superfamily / Rubella membrane glycoprotein E1 / Rubella membrane glycoprotein E2 / Rubella capsid protein
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesRubella virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 11.1 Å
AuthorsMangala Prasad, V. / Klose, T. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095366 United States
CitationJournal: 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.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Experimental preparation
Category: em_sample_support / pdbx_audit_support
Item: _em_sample_support.grid_type / _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
A: E1 glycoprotein


Theoretical massNumber of molelcules
Total (without water)50,5731
Polymers50,5731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20940 Å2

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Components

#1: Protein E1 glycoprotein / p110


Mass: 50573.352 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 583-1018)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubella virus / Production host: Cercopithecus aethiops (grivet) / References: UniProt: P08563

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Rubella virus E1-E2 glycoprotein spike / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.085 MDa / Experimental value: NO
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
10.02 MTrisC4H11NO31
20.12 Msodium chlorideNaClSodium chloride1
30.001 MEDTAEthylenediaminetetraacetic acidC10H16N2O81
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Rubella virus was purified from Vero cells. Glycoprotein spike volumes were extracted from the surface of virus tomograms.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 11000 X / Nominal defocus max: 500 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1IMOD/PEET4.8.40/1.11.0volume selection
2LeginonTomgraphy 3.1image acquisition
4IMOD4.8.40CTF correction
7EMfitmodel fitting
11PEET1.11.0final Euler assignment
12PEET1.11.0classification
13PEET1.11.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7290 / Symmetry type: POINT
EM volume selectionMethod: manual picking / Num. of tomograms: 15 / Num. of volumes extracted: 7500
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: sumf
Atomic model buildingPDB-ID: 4ADG

4adg


Pdb chain-ID: A / Pdb chain residue range: 1-421

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