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- PDB-5khe: Fitted structure of rubella virus capsid protein -

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Basic information

Entry
Database: PDB / ID: 5khe
TitleFitted structure of rubella virus capsid protein
Componentscapsid protein
KeywordsVIRAL PROTEIN / rubella virus capsid protein
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / 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 / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / metal ion binding / membrane
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: 35 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 / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: capsid protein
B: capsid protein


Theoretical massNumber of molelcules
Total (without water)60,0332
Polymers60,0332
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5290 Å2
ΔGint-41 kcal/mol
Surface area10400 Å2

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Components

#1: Protein capsid protein


Mass: 30016.332 Da / Num. of mol.: 2 / Fragment: UNP residues 9-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubella virus / Production host: Escherichia coli (E. coli) / References: UniProt: P07566
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 strain M33 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.064 MDa / Experimental value: NO
Source (natural)Organism: Rubella virus strain M33
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) / Plasmid: pTXB1
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
10.5 Msodium chlorideNaCl1
20.05 MTris-ClC4H11NO31
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen 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 FIELD / Nominal magnification: 11000 X / Nominal defocus min: 500 nm
Image recordingElectron dose: 1 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/PEET4.8.40/10.1volume selection
2LeginonTomography 3.1image acquisition
4IMOD4.8.40CTF correction
7EMfitmodel fitting
13PEET10.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 35 Å / Resolution method: OTHER / Num. of particles: 18 / Symmetry type: POINT
EM volume selectionMethod: manual picking / Num. of tomograms: 15 / Num. of volumes extracted: 20 / Reference model: none
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: sumf

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