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- EMDB-1308: Electron cryotomography reveals the portal in the herpesvirus capsid. -

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Basic information

Entry
Database: EMDB / ID: EMD-1308
TitleElectron cryotomography reveals the portal in the herpesvirus capsid.
Map dataThis is the map of the portal.
Sample
  • Sample: Herpes Simplex Virus 1
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsubtomogram averaging / cryo EM
AuthorsChang JT / Schmid MF / Rixon FJ / Chiu W
CitationJournal: J Virol / Year: 2007
Title: Electron cryotomography reveals the portal in the herpesvirus capsid.
Authors: Juan T Chang / Michael F Schmid / Frazer J Rixon / Wah Chiu /
Abstract: Herpes simplex virus type 1 is a human pathogen responsible for a range of illnesses from cold sores to encephalitis. The icosahedral capsid has a portal at one fivefold vertex which, by analogy to ...Herpes simplex virus type 1 is a human pathogen responsible for a range of illnesses from cold sores to encephalitis. The icosahedral capsid has a portal at one fivefold vertex which, by analogy to portal-containing phages, is believed to mediate genome entry and exit. We used electron cryotomography to determine the structure of capsids lacking pentons. The portal vertex appears different from pentons, being located partially inside the capsid shell, a position equivalent to that of bacteriophage portals. Such similarity in portal organization supports the idea of the evolutionary relatedness of these viruses.
History
DepositionNov 25, 2006-
Header (metadata) releaseDec 6, 2006-
Map releaseDec 6, 2007-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1308.gif

Downloads & links

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Map

FileDownload / File: emd_1308.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map of the portal.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.43 Å/pix.
x 288 pix.
= 1563.84 Å		5.43 Å/pix.
x 288 pix.
= 1563.84 Å		5.43 Å/pix.
x 288 pix.
= 1563.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.43 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00526 / Movie #1: 0.08
Minimum - Maximum-0.143747 - 0.406282
Average (Standard dev.)0.0000362704 (±0.00260648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-144-144-144
Dimensions288288288
Spacing288288288
CellA=B=C: 1563.84 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.435.435.43
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z1563.8401563.8401563.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
D min/max/mean-0.1440.4060.000

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Supplemental data

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Sample components

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Entire : Herpes Simplex Virus 1

EntireName: Herpes Simplex Virus 1
Components
  • Sample: Herpes Simplex Virus 1
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #1000: Herpes Simplex Virus 1

SupramoleculeName: Herpes Simplex Virus 1 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human herpesvirus 1

SupramoleculeName: Human herpesvirus 1 / type: virus / ID: 1 / Name.synonym: Herpes Simplex / NCBI-ID: 10298 / Sci species name: Human herpesvirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: Herpes Simplex
Host (natural)Organism: Homo sapiens (human) / synonym: INVERTEBRATES
Molecular weightExperimental: 888 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 7.2
Details: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 6.8mM CaCl2, 4.9mM MgCl2
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 93 K / Max: 93 K / Average: 93 K
DetailsTilted from -70 to +70 in 2 degree increments using Mr T software (unpublished).
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 50 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 27680 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 20000
Sample stageSpecimen holder: Side entry liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 70 ° / Tilt series - Axis1 - Max angle: 70 °

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Image processing

DetailsDifference map from an average of 13 particles. Average number of tilts used in the 3D reconstructions: 71. Average tomographic tilt angle increment: 2.
Final reconstructionAlgorithm: OTHER / Software - Name: IMOD
Details: Computed the difference map (submission 5138) to visualize the portal.

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