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- EMDB-3361: HSV bubblegram imaging -

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Basic information

Entry
Database: EMDB / ID: EMD-3361
TitleHSV bubblegram imaging
Map datareconstruction of HSV C-Capsid at 15th exposure
Sample
  • Sample: Herpes Simplex Virus Type 1
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)
KeywordsHSV / Herpes Simplex Virus / Bubblegram / Radiation Damage / C-capsid
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsWu W / Newcomb WW / Cheng N / Aksyuk A / Winkler DC / Steven AC
CitationJournal: J Virol / Year: 2016
Title: Internal Proteins of the Procapsid and Mature Capsids of Herpes Simplex Virus 1 Mapped by Bubblegram Imaging.
Authors: Weimin Wu / William W Newcomb / Naiqian Cheng / Anastasia Aksyuk / Dennis C Winkler / Alasdair C Steven /
Abstract: The herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. ...The herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. First, a procapsid is formed through coassembly of the surface shell with an inner scaffolding shell; then the procapsid matures via a major structural transformation, triggered by limited proteolysis of the scaffolding proteins. Three mature capsids are found in the nuclei of infected cells. A capsids are empty, B capsids retain a shrunken scaffolding shell, and C capsids-which develop into infectious virions-are filled with DNA and ostensibly have expelled the scaffolding shell. The possible presence of other internal proteins in C capsids has been moot as, in cryo-electron microscopy (cryo-EM), they would be camouflaged by the surrounding DNA. We have used bubblegram imaging to map internal proteins in all four capsids, aided by the discovery that the scaffolding protein is exceptionally prone to radiation-induced bubbling. We confirmed that this protein forms thick-walled inner shells in the procapsid and the B capsid. C capsids generate two classes of bubbles: one occupies positions beneath the vertices of the icosahedral surface shell, and the other is distributed throughout its interior. A likely candidate is the viral protease. A subpopulation of C capsids bubbles particularly profusely and may represent particles in which expulsion of scaffold and DNA packaging are incomplete. Based on the procapsid structure, we propose that the axial channels of hexameric capsomers afford the pathway via which the scaffolding protein is expelled.
IMPORTANCE: In addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are ...IMPORTANCE: In addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are difficult to locate within the virion. A novel adaptation of cryo-EM based on detecting gas bubbles generated by radiation damage was used to localize internal proteins of HSV-1, yielding insights into how capsid maturation is regulated. The scaffolding protein, which forms inner shells in the procapsid and B capsid, is exceptionally bubbling-prone. In the mature DNA-filled C capsid, a previously undetected protein was found to underlie the icosahedral vertices: this is tentatively assigned as a storage form of the viral protease. We also observed a capsid species that appears to contain substantial amounts of scaffolding protein as well as DNA, suggesting that DNA packaging and expulsion of the scaffolding protein are coupled processes.
History
DepositionMar 3, 2016-
Header (metadata) releaseApr 13, 2016-
Map releaseApr 13, 2016-
UpdateMay 18, 2016-
Current statusMay 18, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13300
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 13300
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3361.png

Downloads & links

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Map

FileDownload / File: emd_3361.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of HSV C-Capsid at 15th exposure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.68 Å/pix.
x 240 pix.
= 1604.16 Å		6.68 Å/pix.
x 240 pix.
= 1604.16 Å		6.68 Å/pix.
x 240 pix.
= 1604.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.684 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13300.0 / Movie #1: 13300
Minimum - Maximum-120331.609375 - 43738.00390625
Average (Standard dev.)-407.744873050000024 (±7312.154785159999847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 1604.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.6846.6846.684
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z1604.1601604.1601604.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-120331.60943738.004-407.745

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Supplemental data

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Sample components

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Entire : Herpes Simplex Virus Type 1

EntireName: Herpes Simplex Virus Type 1 (Herpes simplex virus type 1)
Components
  • Sample: Herpes Simplex Virus Type 1
  • Virus: Human herpesvirus 1 (Herpes simplex virus type 1)

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Supramolecule #1000: Herpes Simplex Virus Type 1

SupramoleculeName: Herpes Simplex Virus Type 1 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human herpesvirus 1

SupramoleculeName: Human herpesvirus 1 / type: virus / ID: 1 / NCBI-ID: 10298 / Sci species name: Human herpesvirus 1 / Sci species strain: HSV-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Cricetulus griseus (Chinese hamster) / Recombinant strain: 17MP / Recombinant cell: BHK-21

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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

VitrificationCryogen name: NITROGEN / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateMay 12, 2014
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: 18 / Average electron dose: 225 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: average of particles
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN / Details: We are not aiming at resolution. / Number images used: 235

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