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- EMDB-2352: Structure of the Bunyamwera virus glycoprotein spike determined b... -

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Basic information

Entry
Database: EMDB / ID: EMD-2352
TitleStructure of the Bunyamwera virus glycoprotein spike determined by electron cryo-tomography and sub-volume averaging
Map dataSub-tomogram average of Bunyamwera virus glycoprotein spike
Sample
  • Sample: Purified Bunyamwera virus particles
  • Protein or peptide: Bunyamwera virus glycoprotein Gn-Gc membrane complex
KeywordsBunyavirus / viral glycoprotein / reconstruction / viral fusion / orthobunyavirus
Biological speciesBunyamwera virus
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsBowden TA / Bitto D / McLees A / Yeromonahos C / Elliott RM / Huiskonen JT
CitationJournal: PLoS Pathog / Year: 2013
Title: Orthobunyavirus ultrastructure and the curious tripodal glycoprotein spike.
Authors: Thomas A Bowden / David Bitto / Angela McLees / Christelle Yeromonahos / Richard M Elliott / Juha T Huiskonen /
Abstract: The genus Orthobunyavirus within the family Bunyaviridae constitutes an expanding group of emerging viruses, which threaten human and animal health. Despite the medical importance, little is known ...The genus Orthobunyavirus within the family Bunyaviridae constitutes an expanding group of emerging viruses, which threaten human and animal health. Despite the medical importance, little is known about orthobunyavirus structure, a prerequisite for understanding virus assembly and entry. Here, using electron cryo-tomography, we report the ultrastructure of Bunyamwera virus, the prototypic member of this genus. Whilst Bunyamwera virions are pleomorphic in shape, they display a locally ordered lattice of glycoprotein spikes. Each spike protrudes 18 nm from the viral membrane and becomes disordered upon introduction to an acidic environment. Using sub-tomogram averaging, we derived a three-dimensional model of the trimeric pre-fusion glycoprotein spike to 3-nm resolution. The glycoprotein spike consists mainly of the putative class-II fusion glycoprotein and exhibits a unique tripod-like arrangement. Protein-protein contacts between neighbouring spikes occur at membrane-proximal regions and intra-spike contacts at membrane-distal regions. This trimeric assembly deviates from previously observed fusion glycoprotein arrangements, suggesting a greater than anticipated repertoire of viral fusion glycoprotein oligomerization. Our study provides evidence of a pH-dependent conformational change that occurs during orthobunyaviral entry into host cells and a blueprint for the structure of this group of emerging pathogens.
History
DepositionApr 5, 2013-
Header (metadata) releaseMay 1, 2013-
Map releaseMay 22, 2013-
UpdateJun 5, 2013-
Current statusJun 5, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2352.png

Downloads & links

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Map

FileDownload / File: emd_2352.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of Bunyamwera virus glycoprotein spike
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.4 Å/pix.
x 100 pix.
= 540. Å		5.4 Å/pix.
x 100 pix.
= 540. Å		5.4 Å/pix.
x 100 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.59051943 - 5.82957029
Average (Standard dev.)0.0 (±0.55824095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-4.5915.8300.000

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Supplemental data

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Sample components

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Entire : Purified Bunyamwera virus particles

EntireName: Purified Bunyamwera virus particles
Components
  • Sample: Purified Bunyamwera virus particles
  • Protein or peptide: Bunyamwera virus glycoprotein Gn-Gc membrane complex

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Supramolecule #1000: Purified Bunyamwera virus particles

SupramoleculeName: Purified Bunyamwera virus particles / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Bunyamwera virus glycoprotein Gn-Gc membrane complex

MacromoleculeName: Bunyamwera virus glycoprotein Gn-Gc membrane complex / type: protein_or_peptide / ID: 1 / Name.synonym: Bunyamwera viral glycoprotein spike
Details: One central trimeric spike surrounded by six neighbouring spikes
Recombinant expression: No
Source (natural)Organism: Bunyamwera virus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 10 mM Tris pH 7.4, 100 mM NaCl
GridDetails: C-flat CF-2/1/2C
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber temperature: 103 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot both sides for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 100 K / Max: 120 K / Average: 100 K
Specialist opticsEnergy filter - Name: GIF2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsLow dose tomography
DateMar 28, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 100 e/Å2
Details: Thirteen single-axis tilt series were collected over an angular range of -60 to 60 at 3 degree increments.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 111111 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Details2,000 subtomograms were selected using template matching in Jsubtomo
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: Jsubtomo
Details: Final map was calculated by averaging the two half maps. A low pass filter to 30 A was applied.
Number subtomograms used: 2000
CTF correctionDetails: Low pass filter was applied after the first zero of the CTF

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