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- EMDB-5650: Pseudorabies virus C-capsid from cryo-electron microscopy -

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Basic information

Entry
Database: EMDB / ID: EMD-5650
TitlePseudorabies virus C-capsid from cryo-electron microscopy
Map dataReconstruction of pseudorabies virus (PRV) C-capsid
Sample
  • Sample: Pseudorabies virus (PRV) C-capsid
  • Virus: Suid herpesvirus 1
Keywordsherpesvirus / capsid
Biological speciesSuid herpesvirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsHoma FL / Huffman JB / Toropova K / Lopez HR / Makhov AM / Conway JF
CitationJournal: J Mol Biol / Year: 2013
Title: Structure of the pseudorabies virus capsid: comparison with herpes simplex virus type 1 and differential binding of essential minor proteins.
Authors: F L Homa / J B Huffman / K Toropova / H R Lopez / A M Makhov / J F Conway /
Abstract: The structure of pseudorabies virus (PRV) capsids isolated from the nucleus of infected cells and from PRV virions was determined by cryo-electron microscopy (cryo-EM) and compared to herpes simplex ...The structure of pseudorabies virus (PRV) capsids isolated from the nucleus of infected cells and from PRV virions was determined by cryo-electron microscopy (cryo-EM) and compared to herpes simplex virus type 1 (HSV-1) capsids. PRV capsid structures closely resemble those of HSV-1, including distribution of the capsid vertex specific component (CVSC) of HSV-1, which is a heterodimer of the pUL17 and pUL25 proteins. Occupancy of CVSC on all PRV capsids is near 100%, compared to ~50% reported for HSV-1 C-capsids and 25% or less that we measure for HSV-1 A- and B-capsids. A PRV mutant lacking pUL25 does not produce C-capsids and lacks visible CVSC density in the cryo-EM-based reconstruction. A reconstruction of PRV capsids in which green fluorescent protein was fused within the N-terminus of pUL25 confirmed previous studies with a similar HSV-1 capsid mutant localizing pUL25 to the CVSC density region that is distal to the penton. However, comparison of the CVSC density in a 9-Å-resolution PRV C-capsid map with the available crystal structure of HSV-1 pUL25 failed to find a satisfactory fit, suggesting either a different fold for PRV pUL25 or a capsid-bound conformation for pUL25 that does not match the X-ray model determined from protein crystallized in solution. The PRV capsid imaged within virions closely resembles C-capsids with the addition of weak but significant density shrouding the pentons that we attribute to tegument proteins. Our results demonstrate significant structure conservation between the PRV and HSV capsids.
History
DepositionMay 1, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseJul 10, 2013-
UpdateSep 4, 2013-
Current statusSep 4, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5650.tif

Downloads & links

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Map

FileDownload / File: emd_5650.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of pseudorabies virus (PRV) C-capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 823 pix.
= 1341.49 Å		1.63 Å/pix.
x 823 pix.
= 1341.49 Å		1.63 Å/pix.
x 823 pix.
= 1341.49 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5000.0 / Movie #1: 5000
Minimum - Maximum-16347.0 - 32443.0
Average (Standard dev.)751.030273439999974 (±3070.181884770000124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions823823823
Spacing823823823
CellA=B=C: 1341.49 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.631.631.63
M x/y/z823823823
origin x/y/z0.0000.0000.000
length x/y/z1341.4901341.4901341.490
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS823823823
D min/max/mean-16347.00032443.000751.030

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Supplemental data

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Sample components

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Entire : Pseudorabies virus (PRV) C-capsid

EntireName: Pseudorabies virus (PRV) C-capsid
Components
  • Sample: Pseudorabies virus (PRV) C-capsid
  • Virus: Suid herpesvirus 1

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Supramolecule #1000: Pseudorabies virus (PRV) C-capsid

SupramoleculeName: Pseudorabies virus (PRV) C-capsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Suid herpesvirus 1

SupramoleculeName: Suid herpesvirus 1 / type: virus / ID: 1 / Name.synonym: pseudorabies virus / Details: C-capsid contains viral dsDNA. / NCBI-ID: 10345 / Sci species name: Suid herpesvirus 1 / Sci species strain: Becker / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: pseudorabies virus
Host (natural)Organism: Sus scrofa (pig) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: C-capsid / Diameter: 1250 Å / T number (triangulation number): 16

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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

BufferpH: 7.5 / Details: TNE: 500mM NaCl, 10mM Tris, 1mM EDTA
GridDetails: Quantifoil R2/1, 200 mesh copper, glow discharged for 10-15 secs
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 95 % / Chamber temperature: 82 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 6 seconds.

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Electron microscopy

MicroscopeFEI POLARA 300
DateJul 18, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 535 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal magnification: 39000
Sample stageSpecimen holder: Polara stage / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected manually with x3dpreprocess.
CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 11908

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