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- EMDB-8249: Subtomogram-averaged map of a single rubella virus capsid unit -

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Basic information

Entry
Database: EMDB / ID: EMD-8249
TitleSubtomogram-averaged map of a single rubella virus capsid unit
Map dataSubtomogram-averaged single capsid unit
Sample
  • Complex: Rubella virus strain M33
    • Protein or peptide: capsid protein
  • Ligand: water
Keywordsrubella virus capsid protein / VIRAL 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 / 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 strain M33 / Rubella virus
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsMangala Prasad V / Klose T
Funding support United States, 1 items
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, 2016-
Header (metadata) releaseJul 13, 2016-
Map releaseMay 10, 2017-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.95
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.95
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5khe
  • Surface level: 1.95
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8249.png

Downloads & links

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Map

FileDownload / File: emd_8249.map.gz / Format: CCP4 / Size: 54.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram-averaged single capsid unit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.28 Å/pix.
x 24 pix.
= 126.72 Å		5.28 Å/pix.
x 24 pix.
= 126.72 Å		5.28 Å/pix.
x 24 pix.
= 126.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.95 / Movie #1: 1.95
Minimum - Maximum-3.2933166 - 4.881808
Average (Standard dev.)0.2174404 (±0.88683295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-12-12-12
Dimensions242424
Spacing242424
CellA=B=C: 126.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.285.285.28
M x/y/z242424
origin x/y/z0.0000.0000.000
length x/y/z126.720126.720126.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-12-12-12
NC/NR/NS242424
D min/max/mean-3.2934.8820.217

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Supplemental data

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Sample components

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Entire : Rubella virus strain M33

EntireName: Rubella virus strain M33
Components
  • Complex: Rubella virus strain M33
    • Protein or peptide: capsid protein
  • Ligand: water

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Supramolecule #1: Rubella virus strain M33

SupramoleculeName: Rubella virus strain M33 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rubella virus strain M33
Molecular weightTheoretical: 64 KDa

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Macromolecule #1: capsid protein

MacromoleculeName: capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rubella virus
Molecular weightTheoretical: 30.016332 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEDLQKALEA QSRALRAELA AGASQSRRPR PPRQRDSSTS GDDSGRDSGG PRRRRGNRGR GQRRDWSRAP PPPEERQETR SQTPAPKPS RAPPQQPQPP RMQTGRGGSA PRPELGPPTN PFQAAVARGL RPPLHDPDTE APTEACVTSW LWSEGEGAVF Y RVDLHFTN ...String:
MEDLQKALEA QSRALRAELA AGASQSRRPR PPRQRDSSTS GDDSGRDSGG PRRRRGNRGR GQRRDWSRAP PPPEERQETR SQTPAPKPS RAPPQQPQPP RMQTGRGGSA PRPELGPPTN PFQAAVARGL RPPLHDPDTE APTEACVTSW LWSEGEGAVF Y RVDLHFTN LGTPPLDEDG RWDPALMYNP CGPEPPAHVV RAYNQPAGDV RGVWGKGERT YAEQDFRVGG TRWHRLLRMP VR GLDGDSA PLPPHTTERI ETRSARHPWR IR

UniProtKB: Structural polyprotein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 35 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
0.5 MNaClsodium chloride
0.05 MC4H11NO3Tris-Cl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.5 µm / Nominal magnification: 11000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Software - Name: PEET (ver. 10.1) / Number subtomograms used: 18
ExtractionNumber tomograms: 15 / Number images used: 20 / Reference model: none / Method: manual picking / Software - Name: IMOD/PEET (ver. 4.8.40/10.1)
Final angle assignmentType: OTHER

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf
Output model

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

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