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

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Basic information

Entry
Database: EMDB / ID: 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.
SampleHerpes simplex virus (type 1 / strain 17)
  • virus
  • Portal
  • Portal-vertex associated tegument protein
SourceHerpes simplex virus (type 1 / strain 17)
Methodsingle particle reconstruction / cryo EM / 7.7 Å resolution
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
DateDeposition: Mar 28, 2018 / Header (metadata) release: Apr 4, 2018 / Map release: Jul 4, 2018 / Last update: Jul 4, 2018

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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 view colored by radius
  • 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4347.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
2.67 Å/pix.
= 1602. Å
600 pix
2.67 Å/pix.
= 1602. Å
600 pix
2.67 Å/pix.
= 1602. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.67 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.1443535 - 0.21554615
Average (Standard dev.)0.00019707222 (0.02158095)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin0.0.0.
Limit599.599.599.
Spacing600600600
CellA=B=C: 1602.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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Sample components

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Entire Herpes simplex virus (type 1 / strain 17)

EntireName: Herpes simplex virus (type 1 / strain 17) / Details: Virus was propagated in BHK cells / Number of components: 3

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

VirusName: Herpes simplex virus (type 1 / strain 17) / Class: VIRION / Details: Virus was propagated in BHK cells / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Herpes simplex virus (type 1 / strain 17)
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Capsid / Diameter: 1250.0 Å / T number(triangulation number): 16

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Component #2: protein, Portal

ProteinName: Portal / Details: Dodecameric portal comprised of the pUL6 protein / Recombinant expression: No
SourceSpecies: Herpes simplex virus (type 1 / strain 17)

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Component #3: protein, Portal-vertex associated tegument protein

ProteinName: Portal-vertex associated tegument protein
Details: portal associated tail-like density comprised of ten copies of the pUL25 protein
Recombinant expression: No
SourceSpecies: Herpes simplex virus (type 1 / strain 17)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: Phosphate buffered saline / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 78 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3702
Details: Images were acquired as 40 fractions per micrograph at 1.78 angstroms/pixel sampling.
Raw dataEMPIAR-10189 (Title: Structure of the herpes-simplex virus portal-vertex / Data size: 238.6
Data #1: Motion corrected micrographs of herpes simplex virus type 1 virions [micrographs - single frame])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C5 (5 fold cyclic) / Number of projections: 5337
Details: Images were motion-corrected using motioncor2 Defocus estimation was performed using GCTF
3D reconstructionAlgorithm: BACK PROJECTION
CTF correction: CTF correction was implemented through Relion
Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF
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.
FSC plot
(resolution estimation)

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