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- EMDB-5147: Bluetongue virus structure reveals a sialic acid binding domain, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5147
TitleBluetongue virus structure reveals a sialic acid binding domain, amphipathic helices and a central coiled coil in the outer capsid proteins
Map dataBTV map
Sample
  • Sample: Bluetongue Virus
  • Virus: Bluetongue virus
KeywordsBluetongue virus cryoEM sialic acid
Function / homology
Function and homology information


viral inner capsid / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / structural molecule activity
Similarity search - Function
Outer capsid protein VP2, Orbivirus / Orbivirus outer capsid protein VP2 / Outer capsid protein VP5, Orbivirus / Orbivirus outer capsid protein VP5
Similarity search - Domain/homology
Outer capsid protein VP2 / Outer capsid protein VP5
Similarity search - Component
Biological speciesBluetongue virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.0 Å
AuthorsZhang X / Boyce M / Bhattacharya B / Schein S / Roy P / Zhou ZH
CitationJournal: Proc Natl Acad Sci U S A / Year: 2010
Title: Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins.
Authors: Xing Zhang / Mark Boyce / Bishnupriya Bhattacharya / Xiaokang Zhang / Stan Schein / Polly Roy / Z Hong Zhou /
Abstract: Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: ...Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: a well-studied, stable core enclosing the dsRNA genome and a highly unstable, poorly studied coat responsible for host cell attachment and entry. Here, based on cryo-electron microscopy (cryoEM), we report a 7-A resolution structure of the infectious BTV virion, including the coat proteins. We show that unlike other dsRNA viruses, the VP2 attachment trimer has a triskelion shape composed of three tip domains branching from a central hub domain. We identify three putative sialic acid-binding pockets in the hub and present supporting biochemical data indicating sugar moiety binding is important for BTV infection. Despite being a nonenveloped virus, the putative VP5 membrane penetration trimer, located slightly inward of the VP2 attachment trimer, has a central coiled-coil alpha-helical bundle, similar to the fusion proteins of many enveloped viruses (e.g., HIV, herpesviruses, vesicular stomatitis virus, and influenza virus). Moreover, mapping of the amino acid sequence of VP5 to the secondary structural elements identified by cryoEM locates 15 amphipathic alpha-helical regions on the external surface of each VP5 trimer. The cryoEM density map also reveals few, weak interactions between the VP5 trimer and both the outer-coat VP2 trimer and the underlying core VP7 trimer, suggesting that the surface of VP5 could unfurl like an umbrella during penetration and shedding of the coat to release the transcriptionally active core particle.
History
DepositionDec 9, 2009-
Header (metadata) releaseDec 16, 2009-
Map releaseMar 30, 2010-
UpdateDec 26, 2012-
Current statusDec 26, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iyk
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5147_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5147.map.gz / Format: CCP4 / Size: 465.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBTV map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 500 pix.
= 940. Å		1.88 Å/pix.
x 500 pix.
= 940. Å		1.88 Å/pix.
x 500 pix.
= 940. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.08033805 - 0.12581272
Average (Standard dev.)-0.00302703 (±0.02796235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 940.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.881.881.88
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z940.000940.000940.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS500500500
D min/max/mean-0.0800.126-0.003

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Supplemental data

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Segmentation: BTV VP2

AnnotationBTV VP2
Fileemd_5147_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Segmentation: averaged VP5

Annotationaveraged VP5
Fileemd_5147_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bluetongue Virus

EntireName: Bluetongue Virus
Components
  • Sample: Bluetongue Virus
  • Virus: Bluetongue virus

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Supramolecule #1000: Bluetongue Virus

SupramoleculeName: Bluetongue Virus / type: sample / ID: 1000 / Details: The sample was monodisperse in ice / Oligomeric state: Icosahedron / Number unique components: 4

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Supramolecule #1: Bluetongue virus

SupramoleculeName: Bluetongue virus / type: virus / ID: 1 / Name.synonym: Bluetongue Virus / NCBI-ID: 40051 / Sci species name: Bluetongue virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Bluetongue Virus
Host (natural)Organism: livestock (unknown) / synonym: VERTEBRATES

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: PBS
StainingType: NEGATIVE / Details: -175C
GridDetails: 400 mesh Lacey carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 90 K
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 15 µm / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79787 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 80000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Frealign IMIRS

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