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- EMDB-1886: The 6A cryo-EM reconstruction of Barmah Forest virus -

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Basic information

Entry
Database: EMDB / ID: EMD-1886
TitleThe 6A cryo-EM reconstruction of Barmah Forest virus
Map dataA 3D reconstruction map of Barmah Forest virus
Sample
  • Sample: Barmah Forest virus
  • Virus: Barmah Forest virus
KeywordsAlphavirus / icosahedral
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesBarmah Forest virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 6.0 Å
AuthorsKostyuchenko VA / Jakana J / Liu X / Haddow AD / Aung M / Weaver SC / Chiu W / Lok SM
CitationJournal: J Virol / Year: 2011
Title: The structure of barmah forest virus as revealed by cryo-electron microscopy at a 6-angstrom resolution has detailed transmembrane protein architecture and interactions.
Authors: Victor A Kostyuchenko / Joanita Jakana / Xiangan Liu / Andrew D Haddow / Myint Aung / Scott C Weaver / Wah Chiu / Shee-Mei Lok /
Abstract: Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, ...Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, with RNA-containing nucleocapsid surrounded by a bilipid membrane anchored with the surface proteins E1 and E2. The map allows details of the transmembrane regions of E1 and E2 to be seen. The C-terminal end of the E2 transmembrane helix binds to the capsid protein. Following the E2 transmembrane helix, a short α-helical endodomain lies on the inner surface of the lipid envelope. The E2 endodomain interacts with E1 transmembrane helix from a neighboring E1-E2 trimeric spike, thereby acting as a spacer and a linker between spikes. In agreement with previous mutagenesis studies, the endodomain plays an important role in recruiting other E1-E2 spikes to the budding site during virus assembly. The E2 endodomain may thus serve as a target for antiviral drug design.
History
DepositionMar 16, 2011-
Header (metadata) releaseAug 12, 2011-
Map releaseJan 27, 2012-
UpdateOct 12, 2016-
Current statusOct 12, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2yew
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2yew
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1886.png

Downloads & links

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Map

FileDownload / File: emd_1886.map.gz / Format: CCP4 / Size: 711.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA 3D reconstruction map of Barmah Forest virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 576 pix.
= 817.92 Å		1.42 Å/pix.
x 576 pix.
= 817.92 Å		1.42 Å/pix.
x 576 pix.
= 817.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 5.0 / Movie #1: 6
Minimum - Maximum-20.788326260000002 - 29.373136519999999
Average (Standard dev.)0.0 (±2.50054336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-288-288-288
Dimensions576576576
Spacing576576576
CellA=B=C: 817.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z576576576
origin x/y/z0.0000.0000.000
length x/y/z817.920817.920817.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-288-288-288
NC/NR/NS576576576
D min/max/mean-20.78829.3730.000

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Supplemental data

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Sample components

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Entire : Barmah Forest virus

EntireName: Barmah Forest virus
Components
  • Sample: Barmah Forest virus
  • Virus: Barmah Forest virus

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Supramolecule #1000: Barmah Forest virus

SupramoleculeName: Barmah Forest virus / type: sample / ID: 1000 / Oligomeric state: Whole virion / Number unique components: 1

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Supramolecule #1: Barmah Forest virus

SupramoleculeName: Barmah Forest virus / type: virus / ID: 1 / Name.synonym: BFV / NCBI-ID: 11020 / Sci species name: Barmah Forest virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: BFV
Host (natural)Organism: Culex annulirostris (mosquito) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Name: E1 E2 / Diameter: 350 Å / T number (triangulation number): 4

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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: 7.4 / Details: 0.05M Tris-HCl, pH 7.4, 0.1M NaCl, 0.001M EDTA
StainingType: NEGATIVE / Details: Not stained
GridDetails: Quantifoil grid with thin carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 1 second before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 100 K
DateJan 5, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Number real images: 760 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

DetailsThe particles were selected with ETHAN software, then screened manually
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, MPSA / Number images used: 5169

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Atomic model buiding 1

Initial modelPDB ID:

1svp


Chain - Chain ID: A
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. Initial placement was done manually followed by refinement using Fit in map feature in Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-2yew:
Modeling Barmah Forest virus structural proteins

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Atomic model buiding 2

Initial modelPDB ID:

2xfb


Chain - Chain ID: B
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. Initial placement was done manually followed by refinement using Fit in map feature in Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-2yew:
Modeling Barmah Forest virus structural proteins

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Atomic model buiding 3

Initial modelPDB ID:

2ala


Chain - Chain ID: A
SoftwareName: Chimera
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. Initial placement was done manually followed by refinement using Fit in map feature in Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-2yew:
Modeling Barmah Forest virus structural proteins

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