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- EMDB-1177: Structure of Broadhaven virus by cryoelectron microscopy: correla... -

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Basic information

Entry
Database: EMDB / ID: EMD-1177
TitleStructure of Broadhaven virus by cryoelectron microscopy: correlation of structural and antigenic properties of Broadhaven virus and bluetongue virus outer capsid proteins.
Map data3d reconstruction with phase flipped images
Sample
  • Sample: Broadhaven virus
  • Virus: Broadhaven virus
Biological speciesBroadhaven virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 23.0 Å
AuthorsSchoehn G / Moss SR / Nuttall PA / Hewat EA
CitationJournal: Virology / Year: 1997
Title: Structure of Broadhaven virus by cryoelectron microscopy: correlation of structural and antigenic properties of Broadhaven virus and bluetongue virus outer capsid proteins.
Authors: G Schoehn / S R Moss / P A Nuttall / E A Hewat /
Abstract: The three-dimensional structure of Broadhaven virus (BRDV) has been determined to 23 A resolution by cryoelectron microscopy and image processing. As predicted from sequence homology, the BRDV ...The three-dimensional structure of Broadhaven virus (BRDV) has been determined to 23 A resolution by cryoelectron microscopy and image processing. As predicted from sequence homology, the BRDV structure resembles that of bluetongue virus (BTV) with the notable exception of one of the outer shell proteins. The cores of BRDV and BTV are identical at medium resolution; they have a diameter of 710 A and the VP7 trimers are arranged on a T = 13 icosahedral lattice. The outer shell proteins, VP5 of BRDV and BTV, have roughly the same molecular weight while VP4 of BRDV is only half the molecular weight of the corresponding VP2 of BTV. This size difference allows unambiguous determination of the identity of the triskelion shape as trimers of VP4 of BRDV (VP2 of BTV). The VP4 of BRDV sits on the VP7 trimers and projects outwards 40 A, giving the capsid an overall diameter of 790 A. This contrasts with VP2 of BTV, which projects outwards 95 A to give the capsid a diameter of 900 A. The difference in accessibility of the outer shell proteins of BRDV and BTV correlates with the difference in antigenic properties of these viral proteins. The shape of the BRDV VP5 indicates that it too is a trimer, thus implying that there are 360 copies of VP5 and 180 copies of VP4 per virion.
History
DepositionOct 21, 2005-
Header (metadata) releaseNov 4, 2005-
Map releaseNov 7, 2005-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 90
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 90
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1177.gif

Downloads & links

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Map

FileDownload / File: emd_1177.map.gz / Format: CCP4 / Size: 18.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3d reconstruction with phase flipped images
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.09 Å/pix.
x 170 pix.
= 865.3 Å		5.09 Å/pix.
x 170 pix.
= 865.3 Å		5.09 Å/pix.
x 170 pix.
= 865.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.09 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 130.0 / Movie #1: 90
Minimum - Maximum-374.79000000000002 - 300.619000000000028
Average (Standard dev.)12.0206 (±58.799799999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions170170170
Spacing170170170
CellA=B=C: 865.3 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.095.095.09
M x/y/z170170170
origin x/y/z0.0000.0000.000
length x/y/z865.300865.300865.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-77-770
NX/NY/NZ15515578
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS170170170
D min/max/mean-374.790300.61912.021

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Supplemental data

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Sample components

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Entire : Broadhaven virus

EntireName: Broadhaven virus
Components
  • Sample: Broadhaven virus
  • Virus: Broadhaven virus

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Supramolecule #1000: Broadhaven virus

SupramoleculeName: Broadhaven virus / type: sample / ID: 1000 / Details: Virus grown in BHK cells and purified / Number unique components: 1

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Supramolecule #1: Broadhaven virus

SupramoleculeName: Broadhaven virus / type: virus / ID: 1 / NCBI-ID: 10893 / Sci species name: Broadhaven virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: sea bird (butterflies/moths) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: triple shell / Diameter: 800 Å / T number (triangulation number): 13

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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

Concentration0.5 mg/mL
StainingType: NEGATIVE
Details: Cryo EM on home made holey grids covered by a thin layer of carbon
GridDetails: 400 mesh grid
VitrificationCryogen name: ETHANE / Instrument: OTHER
Details: Vitrification instrument: zeiss. on holey grid covered by carbon to increase the concentration

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 27500
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000
DateFeb 12, 1996
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 10 / Average electron dose: 9 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: pft / Number images used: 200

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