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- EMDB-1956: Cryo Electron Tomography of Herpes Simplex Virus during Axonal Tr... -

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Entry
Database: EMDB / ID: EMD-1956
TitleCryo Electron Tomography of Herpes Simplex Virus during Axonal Transport and Secondary Envelopment in Primary Neurons
Map dataHerpes simplex virus 1 cytosolic C-capsid
Sample
  • Sample: Herpes simplex virus 1 cytosolic C-capsid
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)
KeywordsHSV-1 / HSV1 / herpesvirus / herpes simplex virus 1 / capsid / cytosolic C-capsid / tegument
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsubtomogram averaging / cryo EM / negative staining / Resolution: 69.0 Å
AuthorsIbiricu I / Huiskonen JT / Doehner K / Bradke F / Sodeik B / Gruenewald K
CitationJournal: PLoS Pathog / Year: 2011
Title: Cryo electron tomography of herpes simplex virus during axonal transport and secondary envelopment in primary neurons.
Authors: Iosune Ibiricu / Juha T Huiskonen / Katinka Döhner / Frank Bradke / Beate Sodeik / Kay Grünewald /
Abstract: During herpes simplex virus 1 (HSV1) egress in neurons, viral particles travel from the neuronal cell body along the axon towards the synapse. Whether HSV1 particles are transported as enveloped ...During herpes simplex virus 1 (HSV1) egress in neurons, viral particles travel from the neuronal cell body along the axon towards the synapse. Whether HSV1 particles are transported as enveloped virions as proposed by the 'married' model or as non-enveloped capsids suggested by the 'separate' model is controversial. Specific viral proteins may form a recruitment platform for microtubule motors that catalyze such transport. However, their subviral location has remained elusive. Here we established a system to analyze herpesvirus egress by cryo electron tomography. At 16 h post infection, we observed intra-axonal transport of progeny HSV1 viral particles in dissociated hippocampal neurons by live-cell fluorescence microscopy. Cryo electron tomography of frozen-hydrated neurons revealed that most egressing capsids were transported independently of the viral envelope. Unexpectedly, we found not only DNA-containing capsids (cytosolic C-capsids), but also capsids lacking DNA (cytosolic A-/B-capsids) in mid-axon regions. Subvolume averaging revealed lower amounts of tegument on cytosolic A-/B-capsids than on C-capsids. Nevertheless, all capsid types underwent active axonal transport. Therefore, even few tegument proteins on the capsid vertices seemed to suffice for transport. Secondary envelopment of capsids was observed at axon terminals. On their luminal face, the enveloping vesicles were studded with typical glycoprotein-like spikes. Furthermore, we noted an accretion of tegument density at the concave cytosolic face of the vesicle membrane in close proximity to the capsids. Three-dimensional analysis revealed that these assembly sites lacked cytoskeletal elements, but that filamentous actin surrounded them and formed an assembly compartment. Our data support the 'separate model' for HSV1 egress, i.e. progeny herpes viruses being transported along axons as subassemblies and not as complete virions within transport vesicles.
History
DepositionSep 2, 2011-
Header (metadata) releaseSep 30, 2011-
Map releaseAug 29, 2012-
UpdateSep 5, 2012-
Current statusSep 5, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Map

FileDownload / File: emd_1956.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHerpes simplex virus 1 cytosolic C-capsid
Voxel sizeX=Y=Z: 8.05 Å
Density
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-4.5026927 - 4.92666101
Average (Standard dev.)-0.1740697 (±1.00548768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-101-101-101
Dimensions200200200
Spacing200200200
CellA=B=C: 1610.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.058.058.05
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1610.0001610.0001610.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-101-101-101
NC/NR/NS200200200
D min/max/mean-4.5034.927-0.174

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Supplemental data

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Sample components

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Entire : Herpes simplex virus 1 cytosolic C-capsid

EntireName: Herpes simplex virus 1 cytosolic C-capsid
Components
  • Sample: Herpes simplex virus 1 cytosolic C-capsid
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #1000: Herpes simplex virus 1 cytosolic C-capsid

SupramoleculeName: Herpes simplex virus 1 cytosolic C-capsid / type: sample / ID: 1000 / Oligomeric state: Icosahedral Capsid / 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 virus 1 / NCBI-ID: 10298 / Sci species name: Human herpesvirus 1 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Herpes simplex virus 1
Host (natural)Organism: Rattus norvegicus (Norway rat) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1250 Å / T number (triangulation number): 16

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Details: unstained
GridDetails: 200 mesh Au grids with holey carbon support film (Au R2/1 200 mesh, Quantifoil
VitrificationCryogen name: ETHANE / Instrument: OTHER / Method: Manual blotting

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37267 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 12.0 µm / Nominal defocus min: 10.0 µm / Nominal magnification: 27500
Specialist opticsEnergy filter - Name: GIF2002 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
DetailsTilt series
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 80 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Low pass filter
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 69.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD and Bsoft / Details: Map was calculated from tomographic sub-volumes
DetailsSub-volumes of icosahedral particles where manually picked in tomographic reconstructions, aligned and averaged. Average number of projections used in the 3D reconstructions: 41.

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