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- EMDB-4347: Structure of the herpes-simplex virus portal-vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-4347
TitleStructure of the herpes-simplex virus portal-vertex
Map dataReconstruction of the herpes simplex virus type 1 virion, with relaxed (C5) symmetry. The map is sharpened.
Sample
  • Virus: Herpes simplex virus (type 1 / strain 17)
    • Complex: Portal
    • Complex: Portal-vertex associated tegument protein
Biological speciesHerpes simplex virus (type 1 / strain 17)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsMcElwee M / Vijayakrishnan S / Rixon FJ / Bhella D
CitationJournal: PLoS Biol / Year: 2018
Title: Structure of the herpes simplex virus portal-vertex.
Authors: Marion McElwee / Swetha Vijayakrishnan / Frazer Rixon / David Bhella /
Abstract: Herpesviruses include many important human pathogens such as herpes simplex virus, cytomegalovirus, varicella-zoster virus, and the oncogenic Epstein-Barr virus and Kaposi sarcoma-associated ...Herpesviruses include many important human pathogens such as herpes simplex virus, cytomegalovirus, varicella-zoster virus, and the oncogenic Epstein-Barr virus and Kaposi sarcoma-associated herpesvirus. Herpes virions contain a large icosahedral capsid that has a portal at a unique 5-fold vertex, similar to that seen in the tailed bacteriophages. The portal is a molecular motor through which the viral genome enters the capsid during virion morphogenesis. The genome also exits the capsid through the portal-vertex when it is injected through the nuclear pore into the nucleus of a new host cell to initiate infection. Structural investigations of the herpesvirus portal-vertex have proven challenging, owing to the small size of the tail-like portal-vertex-associated tegument (PVAT) and the presence of the tegument layer that lays between the nucleocapsid and the viral envelope, obscuring the view of the portal-vertex. Here, we show the structure of the herpes simplex virus portal-vertex at subnanometer resolution, solved by electron cryomicroscopy (cryoEM) and single-particle 3D reconstruction. This led to a number of new discoveries, including the presence of two previously unknown portal-associated structures that occupy the sites normally taken by the penton and the Ta triplex. Our data revealed that the PVAT is composed of 10 copies of the C-terminal domain of pUL25, which are uniquely arranged as two tiers of star-shaped density. Our 3D reconstruction of the portal-vertex also shows that one end of the viral genome extends outside the portal in the manner described for some bacteriophages but not previously seen in any eukaryote viruses. Finally, we show that the viral genome is consistently packed in a highly ordered left-handed spool to form concentric shells of DNA. Our data provide new insights into the structure of a molecular machine critical to the biology of an important class of human pathogens.
History
DepositionMar 28, 2018-
Header (metadata) releaseApr 4, 2018-
Map releaseJul 4, 2018-
UpdateJul 4, 2018-
Current statusJul 4, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4347_1.png

emd_4347_2.png

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Map

FileDownload / File: emd_4347.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the herpes simplex virus type 1 virion, with relaxed (C5) symmetry. The map is sharpened.
Voxel sizeX=Y=Z: 2.67 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.1443535 - 0.21554615
Average (Standard dev.)0.00019707222 (±0.02158095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 1602.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.672.672.67
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z1602.0001602.0001602.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.1440.2160.000

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Supplemental data

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Additional map: Reconstruction of the herpes simplex virus type 1...

Fileemd_4347_additional.map
AnnotationReconstruction of the herpes simplex virus type 1 virion, with relaxed (C5) symmetry. The map is NOT sharpened.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Herpes simplex virus (type 1 / strain 17)

EntireName: Herpes simplex virus (type 1 / strain 17)
Components
  • Virus: Herpes simplex virus (type 1 / strain 17)
    • Complex: Portal
    • Complex: Portal-vertex associated tegument protein

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Supramolecule #1: Herpes simplex virus (type 1 / strain 17)

SupramoleculeName: Herpes simplex virus (type 1 / strain 17) / type: virus / ID: 1 / Parent: 0 / Details: Virus was propagated in BHK cells / NCBI-ID: 10299 / Sci species name: Herpes simplex virus (type 1 / strain 17) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16

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Supramolecule #2: Portal

SupramoleculeName: Portal / type: complex / ID: 2 / Parent: 1 / Details: Dodecameric portal comprised of the pUL6 protein
Source (natural)Organism: Herpes simplex virus (type 1 / strain 17)

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Supramolecule #3: Portal-vertex associated tegument protein

SupramoleculeName: Portal-vertex associated tegument protein / type: complex / ID: 3 / Parent: 1
Details: portal associated tail-like density comprised of ten copies of the pUL25 protein
Source (natural)Organism: Herpes simplex virus (type 1 / strain 17)

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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

Concentration1 mg/mL
BufferpH: 7.2 / Details: Phosphate buffered saline
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified enveloped virions

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 81000
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3702 / Average exposure time: 12.0 sec. / Average electron dose: 78.0 e/Å2
Details: Images were acquired as 40 fractions per micrograph at 1.78 angstroms/pixel sampling.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12431 / Details: Autopicking in Relion
CTF correctionSoftware - Name: Gctf / Details: CTF correction was implemented through Relion
Startup modelType of model: NONE
Details: Starting model was calculated ab initio in Relion 2.1 assuming full icosahedral symmetry (I2).
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 2.1)
Details: Origin and orientation values were determined by 3D auto refine in RELION, assuming full icosahedral symmetry (i.e. with full gold-standard methods). To compute the C5 symmetric map, we ...Details: Origin and orientation values were determined by 3D auto refine in RELION, assuming full icosahedral symmetry (i.e. with full gold-standard methods). To compute the C5 symmetric map, we performed focussed classification on the refined dataset. Briefly, the symmetry of the dataset was expanded yielding a metadata file in which each particle image had 60 assigned views, corresponding to the 60-fold icosahedral redundancy. A cylindrical mask was prepared in SPIDER, that covered a single five-fold vertex. 3D classification in RELION was then performed, without orientation refinement (k=10). This led to the definition of a single class in which we could see the portal-vertex associated tegument (tail). The above analysis was performed on data with 5x binning. The final reconstruction was calculated using 1.5x binned data. The portal-vertex class comprised 26,891 views from 5,337 particle images. Particle images contributed a median 5 views each, thus C5 symmetry is assumed to be applied.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1)
Details: Following definition of the class that featured the unique portal vertex, the metadata file was parsed to change sampling from 5x binning to 1.5x binning, and divide the dataset into two ...Details: Following definition of the class that featured the unique portal vertex, the metadata file was parsed to change sampling from 5x binning to 1.5x binning, and divide the dataset into two halves. Half-maps were calculated and processed to evaluate the FSC and for b-factor estimation.
Number images used: 5337
DetailsImages were motion-corrected using motioncor2 Defocus estimation was performed using GCTF
FSC plot (resolution estimation)

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