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- EMDB-1307: Electron cryotomography reveals the portal in the herpesvirus capsid. -

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Basic information

Entry
Database: EMDB / ID: 1307
TitleElectron cryotomography reveals the portal in the herpesvirus capsid.
SampleHerpes Simplex Virus 1
SourceHuman herpesvirus 1 / virus / Herpes Simplex / ヒトヘルペスウイルス 1
Map dataThis is the 5-fold-averaged map.
Methodsubtomogram averaging
AuthorsChang JT / Schmid MF / Rixon FJ / Chiu W
CitationJ. Virol., 2007, 81, 2065-2068

J. Virol., 2007, 81, 2065-2068 StrPapers
Electron cryotomography reveals the portal in the herpesvirus capsid.
Juan T Chang / Michael F Schmid / Frazer J Rixon / Wah Chiu

DateDeposition: Nov 25, 2006 / Header (metadata) release: Dec 6, 2006 / Map release: Dec 6, 2007 / Last update: Nov 25, 2006

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1307.map.gz (map file in CCP4 format, 93313 KB)
Projections & slices
Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
5.43 A/pix
= 1563.84 A
288 pix
5.43 A/pix
= 1563.84 A
288 pix
5.43 A/pix
= 1563.84 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.43 A
Density
Contour Level:0.119, 0.12 (movie #1):
Minimum - Maximum-0.232214 - 0.370385
Average (Standard dev.)-0.0147267 (0.0501588)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin-144-144-144
Limit143143143
Spacing288288288
CellA=B=C: 1563.84 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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-0.2320.370-0.015

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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 / Number of components: 1

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Component #1: virus, Human herpesvirus 1

VirusName: Human herpesvirus 1 / a.k.a: Herpes Simplex / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Human herpesvirus 1 / virus / Herpes Simplex / ヒトヘルペスウイルス 1
Source (natural)Host Species: Homo sapiens / human / Host category: INVERTEBRATES
Shell #1Name of element: Capsid / Diameter: 1250 A / T number(triangulation number): 16

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Experimental details

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Sample preparation

Sample solutionBuffer solution: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 6.8mM CaCl2, 4.9mM MgCl2
pH: 7.2
Support film200 mesh copper grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 100 % / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F
Details: Tilted from -70 to +70 in 2 degree increments using Mr T software (unpublished).
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 20000 X (nominal), 27680 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 nm
Specimen HolderHolder: Side entry liquid nitrogen cooled / Model: GATAN LIQUID NITROGEN / Tilt Angle: 70 - 70 deg. / Temperature: 93 K ( 93 - 93 K)
CameraDetector: GENERIC GATAN

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Image processing

ProcessingMethod: subtomogram averaging
Details: Averaged 13 particles extracted from the reconstruction. Average number of tilts used in the 3D reconstructions: 71. Average tomographic tilt angle increment: 2.
3D reconstructionAlgorithm: Weighted backprojection / Software: IMOD / Details: 5-fold-averaged

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