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- EMDB-8248: Subtomogram-averaged surface glycoprotein spike density of rubell... -

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Basic information

Entry
Database: EMDB / ID: EMD-8248
TitleSubtomogram-averaged surface glycoprotein spike density of rubella virus
Map dataSub-tomogram averaged surface glycoprotein spike density of rubella virus
Sample
  • Complex: Rubella virus E1-E2 glycoprotein spike
    • Protein or peptide: E1 glycoprotein
KeywordsRubella virus / surface glycoprotein spike / E1-E2 heterodimer / 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 / 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
Methodsubtomogram averaging / cryo EM / Resolution: 11.1 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-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5khc
  • Surface level: 3.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8248.png

Downloads & links

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Map

FileDownload / File: emd_8248.map.gz / Format: CCP4 / Size: 605.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram averaged surface glycoprotein spike density of rubella virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.64 Å/pix.
x 44 pix.
= 116.16 Å		2.64 Å/pix.
x 80 pix.
= 211.2 Å		2.64 Å/pix.
x 44 pix.
= 116.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.15 / Movie #1: 3.15
Minimum - Maximum-6.344344 - 13.240289000000001
Average (Standard dev.)0.00000000166492 (±2.0180662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions804444
Spacing448044
CellA: 116.16 Å / B: 211.20001 Å / C: 116.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.642.642.64
M x/y/z448044
origin x/y/z0.0000.0000.000
length x/y/z116.160211.200116.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448044
D min/max/mean-6.34413.2400.000

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Supplemental data

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Sample components

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Entire : Rubella virus E1-E2 glycoprotein spike

EntireName: Rubella virus E1-E2 glycoprotein spike
Components
  • Complex: Rubella virus E1-E2 glycoprotein spike
    • Protein or peptide: E1 glycoprotein

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Supramolecule #1: Rubella virus E1-E2 glycoprotein spike

SupramoleculeName: Rubella virus E1-E2 glycoprotein spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 85 KDa

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Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rubella virus
Molecular weightTheoretical: 50.573352 KDa
Recombinant expressionOrganism: Cercopithecus aethiops (grivet)
SequenceString: EEAFTYLCTA PGCATQTPVP VRLAGVRFES KIVDGGCFAP WDLEATGACI CEIPTDVSCE GLGAWVPTAP CARIWNGTQR ACTFWAVNA YSSGGYAQLA SYFNPGGSYY KQYHPTACEV EPAFGHSDAA CWGFPTDTVM SVFALASYVQ HPHKTVRVKF H TETRTVWQ ...String:
EEAFTYLCTA PGCATQTPVP VRLAGVRFES KIVDGGCFAP WDLEATGACI CEIPTDVSCE GLGAWVPTAP CARIWNGTQR ACTFWAVNA YSSGGYAQLA SYFNPGGSYY KQYHPTACEV EPAFGHSDAA CWGFPTDTVM SVFALASYVQ HPHKTVRVKF H TETRTVWQ LSVAGVSCNV TTEHPFCNTP HGQLEVQVPP DPGDLVEYIM NYTGNQQSRW GLGSPNCHGP DWASPVCQRH SP DCSRLVG ATPERPRLRL VDADDPLLRT APGPGEVWVT PVIGSQARKC GLHIRAGPYG HATVEMPEWI HAHTTSDPWH PPG PLGLKF KTVRPVALPR ALAPPRNVRV TGCYQCGTPA LVEGLAPGGG NCHLTVNGED VGAFPPGKFV TAALLNTPPP YQVS CGGES DRASARVIDP AAQSFTGVVY GTHTTAVSET RFEDDDDKAG WSHPQFEKGG GSGGGSGGGS WSHPQFEK

UniProtKB: Structural polyprotein

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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: 8
Component:
ConcentrationFormulaName
0.02 MC4H11NO3Tris
0.12 MNaClsodium chloride
0.001 MC10H16N2O8EDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE
DetailsRubella virus was purified from Vero cells. Glycoprotein spike volumes were extracted from the surface of virus tomograms.

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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: 0.5 µm / Nominal defocus min: 0.4 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: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET (ver. 1.11.0) / Number subtomograms used: 7290
ExtractionNumber tomograms: 15 / Number images used: 7500 / Method: manual picking / Software - Name: IMOD/PEET (ver. 4.8.40/1.11.0)
Final 3D classificationSoftware - Name: PEET (ver. 1.11.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: PEET (ver. 1.11.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4adg


Chain - Chain ID: A / Chain - Residue range: 1-421 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf
Output model

PDB-5khc:
Structure of rubella virus E1 glycoprotein ectodomain fitted into sub-tomogram averaged surface spike density of rubella virus

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