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- EMDB-5261: Seeing the Portal in Herpes Simplex Virus type I B-capsids. -

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Basic information

Entry
Database: EMDB / ID: EMD-5261
TitleSeeing the Portal in Herpes Simplex Virus type I B-capsids.
Map datac1 portal density extracted from symmetry free (c1) reconstruction of the HSV-1 B-capsid
Sample
  • Sample: Herpes simplex virus type I B-capsids
  • Virus: Herpes Simplex Virus Type I (Herpes simplex virus type 1)
KeywordsHerpes / HSV1 / Portal / Cryo-EM / Single Particle / UL6 / Asymmetric / Symmetry-free
Biological speciesHerpes Simplex Virus Type I (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsRochat RH / Liu X / Murata K / Nagayama K / Rixon FJ / Chiu W
CitationJournal: J Virol / Year: 2011
Title: Seeing the portal in herpes simplex virus type 1 B capsids.
Authors: R H Rochat / X Liu / K Murata / K Nagayama / F J Rixon / W Chiu /
Abstract: Resolving the nonicosahedral components in large icosahedral viruses remains a technical challenge in structural virology. We have used the emerging technique of Zernike phase-contrast electron ...Resolving the nonicosahedral components in large icosahedral viruses remains a technical challenge in structural virology. We have used the emerging technique of Zernike phase-contrast electron cryomicroscopy to enhance the image contrast of ice-embedded herpes simplex virus type 1 capsids. Image reconstruction enabled us to retrieve the structure of the unique portal vertex in the context of the icosahedral capsid and, for the first time, show the subunit organization of a portal in a virus infecting eukaryotes. Our map unequivocally resolves the 12-subunit portal situated beneath one of the pentameric vertices, thus removing uncertainty over the location and stoichiometry of the herpesvirus portal.
History
DepositionFeb 16, 2011-
Header (metadata) releaseMar 10, 2011-
Map releaseMar 10, 2011-
UpdateDec 3, 2014-
Current statusDec 3, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5261_1.png

Downloads & links

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Map

FileDownload / File: emd_5261.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationc1 portal density extracted from symmetry free (c1) reconstruction of the HSV-1 B-capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.1 Å/pix.
x 300 pix.
= 1530. Å		5.1 Å/pix.
x 300 pix.
= 1530. Å		5.1 Å/pix.
x 300 pix.
= 1530. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 1
Minimum - Maximum-2.60405159 - 6.89623308
Average (Standard dev.)0.00122184 (±0.05778749)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 1530.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.15.15.1
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z1530.0001530.0001530.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-2.6046.8960.001

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Supplemental data

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Sample components

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Entire : Herpes simplex virus type I B-capsids

EntireName: Herpes simplex virus type I B-capsids
Components
  • Sample: Herpes simplex virus type I B-capsids
  • Virus: Herpes Simplex Virus Type I (Herpes simplex virus type 1)

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Supramolecule #1000: Herpes simplex virus type I B-capsids

SupramoleculeName: Herpes simplex virus type I B-capsids / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1
Molecular weightTheoretical: 100 MDa

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Supramolecule #1: Herpes Simplex Virus Type I

SupramoleculeName: Herpes Simplex Virus Type I / type: virus / ID: 1 / Name.synonym: HSV-1 / Sci species name: Herpes Simplex Virus Type I / Database: NCBI / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: HSV-1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 200 MDa
Virus shellShell ID: 1 / Name: vp5 / Diameter: 1250 Å / T number (triangulation number): 16
Virus shellShell ID: 2 / Name: vp26 / Diameter: 1250 Å / T number (triangulation number): 15
Virus shellShell ID: 3 / Name: vp19 / Diameter: 1250 Å / T number (triangulation number): 10
Virus shellShell ID: 4 / Name: vp23 / Diameter: 1250 Å / T number (triangulation number): 5

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

GridDetails: Quantifoil 2/2 grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 85 K / Instrument: FEI VITROBOT MARK IV / Details: Vitrification instrument: Vitrobot Mark IV / Method: Blot 1 time for 2 seconds

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureMin: 100 K / Max: 101 K / Average: 100 K
Alignment procedureLegacy - Astigmatism: Astigmatism was corrected at 400,000 times magnification
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateJun 10, 2009
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Average electron dose: 20 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 0.2 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Side Entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were aligned using the multi-path simulated annealing algorithm.
CTF correctionDetails: No Correction
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MPSA
Details: Reconstructions were made both with and without imposed symmetry.
Number images used: 6300

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