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- EMDB-8251: Subtomogram-averaged map of in vitro assembled rubella virus caps... -

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Basic information

Entry
Database: EMDB / ID: EMD-8251
TitleSubtomogram-averaged map of in vitro assembled rubella virus capsid protein tetramer complex
Map dataSubtomogram-averaged map of in vitro assembled rubella virus capsid protein tetramer complex, unfiltered and unmasked
Sample
  • Complex: Rubella virus capsid protein
    • Protein or peptide: 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 strain M33
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsMangala Prasad V / Klose T / Rossmann MG
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-
UpdateJun 14, 2017-
Current statusJun 14, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8251.png

Downloads & links

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Map

FileDownload / File: emd_8251.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram-averaged map of in vitro assembled rubella virus capsid protein tetramer complex, unfiltered and unmasked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.28 Å/pix.
x 50 pix.
= 264. Å		5.28 Å/pix.
x 50 pix.
= 264. Å		5.28 Å/pix.
x 50 pix.
= 264. 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: 2. / Movie #1: 2
Minimum - Maximum-4.8632483 - 6.4853272
Average (Standard dev.)-0.000000039384766 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-25-25-25
Dimensions505050
Spacing505050
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.285.285.28
M x/y/z505050
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-25-25-25
NC/NR/NS505050
D min/max/mean-4.8636.485-0.000

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Supplemental data

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Sample components

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Entire : Rubella virus capsid protein

EntireName: Rubella virus capsid protein
Components
  • Complex: Rubella virus capsid protein
    • Protein or peptide: Rubella virus capsid protein

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Supramolecule #1: Rubella virus capsid protein

SupramoleculeName: Rubella virus capsid protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rubella virus strain M33
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta-2 (DE3) / Recombinant plasmid: pTXB1
Molecular weightExperimental: 256 KDa

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Macromolecule #1: Rubella virus capsid protein

MacromoleculeName: Rubella virus capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rubella virus strain M33
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEDLQKALEA QSRALRAELA AGASQSRRPR PPRQRDSSTS GDDSGRDSGG PRRRRGNRGR GQRRDWSRAP PPPEERQETR SQTPAPKPSR APPQQPQPPR MQTGRGGSAP RPELGPPTNP FQAAVARGLR PPLHDPDTEA PTEACVTSWL WSEGEGAVFY RVDLHFTNLG ...String:
MEDLQKALEA QSRALRAELA AGASQSRRPR PPRQRDSSTS GDDSGRDSGG PRRRRGNRGR GQRRDWSRAP PPPEERQETR SQTPAPKPSR APPQQPQPPR MQTGRGGSAP RPELGPPTNP FQAAVARGLR PPLHDPDTEA PTEACVTSWL WSEGEGAVFY RVDLHFTNLG TPPLDEDGRW DPALMYNPCG PEPPAHVVRA YNQPAGDVRG VWGKGERTYA EQDFRVGGTR WHRLLRMPVR GLDGDSAPLP PHTTERIETR SARHPWRIR

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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
0.05 MC4H11NO3Tris
0.5 MNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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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: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.005 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. 1.11.0) / Number subtomograms used: 18
ExtractionNumber tomograms: 15 / Number images used: 20 / Method: manual picking / Software - Name: IMOD/PEEt (ver. 4.8.40/1.11.0)
CTF correctionSoftware - Name: IMOD (ver. 4.8.40)
Final angle assignmentType: OTHER

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