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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 / homologyRubella 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 sourceRubella virus / / virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 11.1 Å resolution
AuthorsMangala Prasad, V. / Klose, T. / Rossmann, M.G.
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2016 / Release: May 10, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 10, 2017Structure modelrepositoryInitial release
1.1Jun 14, 2017Structure modelDatabase referencescitation_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
1.2Sep 13, 2017Structure modelAuthor supporting evidence / Data collectionem_image_scans / pdbx_audit_support_pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: E1 glycoprotein


Theoretical massNumber of molelcules
Total (without water)50,5731
Polyers50,5731
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)0
ΔGint (kcal/M)0
Surface area (Å2)20940

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Components

#1: Protein/peptide E1 glycoprotein / p110


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Rubella virus E1-E2 glycoprotein spike / Type: COMPLEX / Entity ID: 1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.085 deg. / Units: MEGADALTONS / Experimental value: NO
Buffer solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
10.02MTrisC4H11NO31
20.12Msodium chlorideNaCl1
30.001MEDTAC10H16N2O81
SpecimenConc.: 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 supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R 1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: 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 / 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
3D reconstructionResolution: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 7290 / Symmetry type: POINT
EM volume selectionMethod: manual picking / Number of tomograms: 15 / Number of volumes extracted: 7500
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf
Atomic model buildingPDB-ID: 4ADG
Pdb chain ID: A / Pdb chain residue range: 1-421

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