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

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Basic information

Entry
Database: EMDB / ID: 8248
TitleSubtomogram-averaged surface glycoprotein spike density of rubella virus
Map dataSub-tomogram averaged surface glycoprotein spike density of rubella virus
SampleRubella virus E1-E2 glycoprotein spike
  • E1 glycoprotein
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
MethodCryo EM / subtomogram averaging / 11.1 Å resolution
AuthorsMangala Prasad V / Klose T
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 ReportPDB-ID: 5khc

SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: May 10, 2017 / Last update: Sep 13, 2017

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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
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_8248.map.gz (map file in CCP4 format, 620 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.64 Å
Density
Contour Level:3.15 (by author), 3.15 (movie #1):
Minimum - Maximum-6.344344 - 13.240289
Average (Standard dev.)1.66492E-9 (2.0180662)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions804444
Origin000
Limit794343
Spacing448044
CellA: 116.16 Å / B: 211.20001 Å / C: 116.16 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 / Number of components: 2
MassTheoretical: 85 kDa

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Component #1: protein, Rubella virus E1-E2 glycoprotein spike

ProteinName: Rubella virus E1-E2 glycoprotein spike / Recombinant expression: No
MassTheoretical: 85 kDa

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Component #2: protein, E1 glycoprotein

ProteinName: E1 glycoprotein / Recombinant expression: No
MassTheoretical: 50.573352 kDa
Source (engineered)Expression System: Rubella virus / / virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 90 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 11000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 400 - 500 nm
Specimen HolderModel: OTHER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: PEET / Resolution: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: sumf / Refinement space: REAL
Input PDB model: 4ADG
Chain ID: 4ADG_A
Output model

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