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- EMDB-5453: A Tail-like Assembly at the Portal Vertex in Intact Herpes Simple... -

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Basic information

Entry
Database: EMDB / ID: EMD-5453
TitleA Tail-like Assembly at the Portal Vertex in Intact Herpes Simplex Type-1 Virions
Map dataReconstruction of HSV-1 virion using Melon Ball alignment
Sample
  • Sample: Herpes Simplex Virus type 1 (HSV-1) virion.
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)
KeywordsHSV-1 / cryo-ET / cryo-EM / Electron cryo-microscopy / Electron cryo-tomography / PVAT / MSA / Melon Ball / Single Particle Tomography / Sub-tomogram Averaging
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsubtomogram averaging / cryo EM / Resolution: 60.0 Å
AuthorsSchmid MF / Hecksel CW / Rochat RH / Bhella D / Chiu W / Rixon FJ
CitationJournal: PLoS Pathog / Year: 2012
Title: A tail-like assembly at the portal vertex in intact herpes simplex type-1 virions.
Authors: Michael F Schmid / Corey W Hecksel / Ryan H Rochat / David Bhella / Wah Chiu / Frazer J Rixon /
Abstract: Herpes viruses are prevalent and well characterized human pathogens. Despite extensive study, much remains to be learned about the structure of the genome packaging and release machinery in the ...Herpes viruses are prevalent and well characterized human pathogens. Despite extensive study, much remains to be learned about the structure of the genome packaging and release machinery in the capsids of these large and complex double-stranded DNA viruses. However, such machinery is well characterized in tailed bacteriophage, which share a common evolutionary origin with herpesvirus. In tailed bacteriophage, the genome exits from the virus particle through a portal and is transferred into the host cell by a complex apparatus (i.e. the tail) located at the portal vertex. Here we use electron cryo-tomography of human herpes simplex type-1 (HSV-1) virions to reveal a previously unsuspected feature at the portal vertex, which extends across the HSV-1 tegument layer to form a connection between the capsid and the viral membrane. The location of this assembly suggests that it plays a role in genome release into the nucleus and is also important for virion architecture.
History
DepositionJul 30, 2012-
Header (metadata) releaseOct 17, 2012-
Map releaseOct 17, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5453_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5453.map.gz / Format: CCP4 / Size: 159.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HSV-1 virion using Melon Ball alignment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.8 Å/pix.
x 350 pix.
= 3780. Å		10.8 Å/pix.
x 350 pix.
= 3780. Å		10.8 Å/pix.
x 350 pix.
= 3780. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.35 / Movie #1: 4.35
Minimum - Maximum-9.09684944 - 12.58040237
Average (Standard dev.)-0.00761569 (±0.98819494)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-175-175-175
Dimensions350350350
Spacing350350350
CellA=B=C: 3780.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.810.810.8
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z3780.0003780.0003780.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-175-175-175
NC/NR/NS350350350
D min/max/mean-9.09712.580-0.008

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Supplemental data

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Sample components

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Entire : Herpes Simplex Virus type 1 (HSV-1) virion.

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

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Supramolecule #1000: Herpes Simplex Virus type 1 (HSV-1) virion.

SupramoleculeName: Herpes Simplex Virus type 1 (HSV-1) virion. / type: sample / ID: 1000 / Details: Frozen hydrated HSV-1 Virions / Oligomeric state: 1 / Number unique components: 1
Molecular weightTheoretical: 200 MDa

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Supramolecule #1: Human herpesvirus 1

SupramoleculeName: Human herpesvirus 1 / type: virus / ID: 1 / Name.synonym: Herpes Simplex Virus type 1 / Details: Frozen hydrated virions / NCBI-ID: 10298 / Sci species name: Human herpesvirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Herpes Simplex Virus type 1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 200 MDa
Virus shellShell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
Details: 170mM NaCl, 3.4mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 4.9mM MgCl2, 6.8mM CaCl2
GridDetails: Quantifoil R 2/2 holey carbon film on a 200 mesh copper grid, glow discharged in air
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: Manual blotting

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 25.0 eV / Energy filter - Upper energy threshold: 30.0 eV
DateMay 23, 2008
Image recordingCategory: FILM / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Scanner: OTHER / Digitization - Sampling interval: 15 µm / Number real images: 11 / Average electron dose: 88 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 28195 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 20000
Sample stageSpecimen holder: Gatan 914 / Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

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Image processing

DetailsMultivariate Statistical Analysis (MSA) was used to classify a unique vertex in the capsid shell for alignment and averaging. Further details provided in manuscript. Average number of projections used in the 3D reconstructions: 214.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 60.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD, tomohunter / Details: Final map is the average of 214 subvolumes

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