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- EMDB-2092: Three Dimensional Structure of the Epstein-Barr Virus Capsid. -

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Basic information

Entry
Database: EMDB / ID: EMD-2092
TitleThree Dimensional Structure of the Epstein-Barr Virus Capsid.
Map dataEBV capsid purified over CsCl gradient
Sample
  • Sample: Epstein-Barr capsid purified over CsCl gradient
  • Virus: Human herpesvirus 4 (Epstein-Barr virus)
KeywordsStructure / cryo-electron microscopy / Epstein-Barr virus / purification
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 20.0 Å
AuthorsGermi R / Effantin G / Grossi L / Ruigrok RWH / Morand P / Schoehn G
CitationJournal: J Gen Virol / Year: 2012
Title: Three-dimensional structure of the Epstein-Barr virus capsid.
Authors: Raphaele Germi / Gregory Effantin / Laurence Grossi / Rob W H Ruigrok / Patrice Morand / Guy Schoehn /
Abstract: Epstein-Barr virus (EBV), a gammaherpesvirus, infects >90 % of the world's population. Primary infection by EBV can lead to infectious mononucleosis, and EBV persistence is associated with several ...Epstein-Barr virus (EBV), a gammaherpesvirus, infects >90 % of the world's population. Primary infection by EBV can lead to infectious mononucleosis, and EBV persistence is associated with several malignancies. Despite its importance for human health, little structural information is available on EBV. Here we report the purification of the EBV capsid by CsCl- or sucrose density-gradient centrifugation. Cryo-electron microscopy and image analysis resulted in two slightly different three-dimensional structures at about 20 Å resolution. These structures were compared with that of human herpesvirus 8, another gammaherpesvirus. CsCl-gradient purification leads to the removal of part of the triplex complex around the fivefold axes, whereas the complexes between hexons remained in place. This may be due to local differences in stability resulting from variation in quasi-equivalent interactions between pentons and hexons compared with those between hexons only.
History
DepositionMay 4, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1500
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1500
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2092.png

Downloads & links

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Map

FileDownload / File: emd_2092.map.gz / Format: CCP4 / Size: 39.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEBV capsid purified over CsCl gradient
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.5 Å/pix.
x 219 pix.
= 1423.5 Å		6.5 Å/pix.
x 219 pix.
= 1423.5 Å		6.5 Å/pix.
x 219 pix.
= 1423.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1450.0 / Movie #1: 1500
Minimum - Maximum-9426.166015630000402 - 11176.166992189999291
Average (Standard dev.)78.29924011 (±1011.545043950000036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions219219219
Spacing219219219
CellA=B=C: 1423.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.56.56.5
M x/y/z219219219
origin x/y/z0.0000.0000.000
length x/y/z1423.5001423.5001423.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS219219219
D min/max/mean-9426.16611176.16778.299

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Supplemental data

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Sample components

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Entire : Epstein-Barr capsid purified over CsCl gradient

EntireName: Epstein-Barr capsid purified over CsCl gradient
Components
  • Sample: Epstein-Barr capsid purified over CsCl gradient
  • Virus: Human herpesvirus 4 (Epstein-Barr virus)

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Supramolecule #1000: Epstein-Barr capsid purified over CsCl gradient

SupramoleculeName: Epstein-Barr capsid purified over CsCl gradient / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human herpesvirus 4

SupramoleculeName: Human herpesvirus 4 / type: virus / ID: 1
Details: Peripentonal triplex have been removed during purification
NCBI-ID: 10376 / Sci species name: Human herpesvirus 4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: EBV / Diameter: 1250 Å / T number (triangulation number): 16

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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: 0.05 M Tris 0.15 M NaCl, pH 7.4
StainingType: NEGATIVE / Details: Cryo
GridDetails: Quantifoil 300 mesh R2/1 covered by a thin layer of carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5 second before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateJun 3, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 19 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 20000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

Detailspft2 and em3dr2
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: PFT2, em3dr2 / Number images used: 500

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