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- EMDB-9864: Asymmetry reconstruction of HSV-1 virion -

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Basic information

Entry
Database: EMDB / ID: EMD-9864
TitleAsymmetry reconstruction of HSV-1 virion
Map dataHSV-1 virion asymmetry reconstruction
Sample
  • Virus: Human herpesvirus 1 strain KOS
Biological speciesHuman herpesvirus 1 strain KOS
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsLiu YT / Jih J / Dai X / Bi GQ / Zhou ZH
Funding support China, United States, 2 items
OrganizationGrant numberCountry
Other government China
Other government United States
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures of herpes simplex virus type 1 portal vertex and packaged genome.
Authors: Yun-Tao Liu / Jonathan Jih / Xinghong Dai / Guo-Qiang Bi / Z Hong Zhou /
Abstract: Herpesviruses are enveloped viruses that are prevalent in the human population and are responsible for diverse pathologies, including cold sores, birth defects and cancers. They are characterized by ...Herpesviruses are enveloped viruses that are prevalent in the human population and are responsible for diverse pathologies, including cold sores, birth defects and cancers. They are characterized by a highly pressurized pseudo-icosahedral capsid-with triangulation number (T) equal to 16-encapsidating a tightly packed double-stranded DNA (dsDNA) genome. A key process in the herpesvirus life cycle involves the recruitment of an ATP-driven terminase to a unique portal vertex to recognize, package and cleave concatemeric dsDNA, ultimately giving rise to a pressurized, genome-containing virion. Although this process has been studied in dsDNA phages-with which herpesviruses bear some similarities-a lack of high-resolution in situ structures of genome-packaging machinery has prevented the elucidation of how these multi-step reactions, which require close coordination among multiple actors, occur in an integrated environment. To better define the structural basis of genome packaging and organization in herpes simplex virus type 1 (HSV-1), we developed sequential localized classification and symmetry relaxation methods to process cryo-electron microscopy (cryo-EM) images of HSV-1 virions, which enabled us to decouple and reconstruct hetero-symmetric and asymmetric elements within the pseudo-icosahedral capsid. Here we present in situ structures of the unique portal vertex, genomic termini and ordered dsDNA coils in the capsid spooled around a disordered dsDNA core. We identify tentacle-like helices and a globular complex capping the portal vertex that is not observed in phages, indicative of herpesvirus-specific adaptations in the DNA-packaging process. Finally, our atomic models of portal vertex elements reveal how the fivefold-related capsid accommodates symmetry mismatch imparted by the dodecameric portal-a longstanding mystery in icosahedral viruses-and inform possible DNA-sequence recognition and headful-sensing pathways involved in genome packaging. This work showcases how to resolve symmetry-mismatched elements in a large eukaryotic virus and provides insights into the mechanisms of herpesvirus genome packaging.
History
DepositionMar 24, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateJun 26, 2019-
Current statusJun 26, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9864.png

Downloads & links

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Map

FileDownload / File: emd_9864.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHSV-1 virion asymmetry reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 720 pix.
= 1483.2 Å		2.06 Å/pix.
x 720 pix.
= 1483.2 Å		2.06 Å/pix.
x 720 pix.
= 1483.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.03462809 - 0.06849666
Average (Standard dev.)-0.00009110299 (±0.007959081)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 1483.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.062.062.06
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z1483.2001483.2001483.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS720720720
D min/max/mean-0.0350.068-0.000

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Supplemental data

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Sample components

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Entire : Human herpesvirus 1 strain KOS

EntireName: Human herpesvirus 1 strain KOS
Components
  • Virus: Human herpesvirus 1 strain KOS

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Supramolecule #1: Human herpesvirus 1 strain KOS

SupramoleculeName: Human herpesvirus 1 strain KOS / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10306 / Sci species name: Human herpesvirus 1 strain KOS / Sci species strain: KOS / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE
Details: The sample was manually blotted and frozen with a homemade plunger...

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 14000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 45445
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 39939
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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