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- EMDB-8760: Capsid of Pseudorabies virus imaged in intact virions -

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Basic information

Entry
Database: EMDB / ID: EMD-8760
TitleCapsid of Pseudorabies virus imaged in intact virions
Map dataunfiltered map
Sample
  • Virus: Suid herpesvirus 1 (strain Becker)
Biological speciesSuid herpesvirus 1 (strain Becker)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsLiu YT / Jiang J / Bohannon KP / Dai X / Luxton GW / Hui WH / Bi GQ / Smith GA / Zhou ZH
Funding support United States, China, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI056346 United States
National Natural Science Foundation of China (NSFC)313290002 China
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
China Academy of SciencesXDB02050000 China
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: J Gen Virol / Year: 2017
Title: A pUL25 dimer interfaces the pseudorabies virus capsid and tegument.
Authors: Yun-Tao Liu / Jiansen Jiang / Kevin Patrick Bohannon / Xinghong Dai / G W Gant Luxton / Wong Hoi Hui / Guo-Qiang Bi / Gregory Allan Smith / Z Hong Zhou /
Abstract: Inside the virions of α-herpesviruses, tegument protein pUL25 anchors the tegument to capsid vertices through direct interactions with tegument proteins pUL17 and pUL36. In addition to promoting ...Inside the virions of α-herpesviruses, tegument protein pUL25 anchors the tegument to capsid vertices through direct interactions with tegument proteins pUL17 and pUL36. In addition to promoting virion assembly, both pUL25 and pUL36 are critical for intracellular microtubule-dependent capsid transport. Despite these essential roles during infection, the stoichiometry and precise organization of pUL25 and pUL36 on the capsid surface remain controversial due to the insufficient resolution of existing reconstructions from cryo-electron microscopy (cryoEM). Here, we report a three-dimensional (3D) icosahedral reconstruction of pseudorabies virus (PRV), a varicellovirus of the α-herpesvirinae subfamily, obtained by electron-counting cryoEM at 4.9 Å resolution. Our reconstruction resolves a dimer of pUL25 forming a capsid-associated tegument complex with pUL36 and pUL17 through a coiled coil helix bundle, thus correcting previous misinterpretations. A comparison between reconstructions of PRV and the γ-herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) reinforces their similar architectures and establishes important subfamily differences in the capsid-tegument interface.
History
DepositionJun 8, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseNov 1, 2017-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8760.png

Downloads & links

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Map

FileDownload / File: emd_8760.map.gz / Format: CCP4 / Size: 1000 B / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunfiltered map
Voxel sizeX=Y=Z: 1.61 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.02073158 - 0.032964323
Average (Standard dev.)-0.0004562682 (±0.0029965595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-512-512-512
Dimensions102410241024
Spacing102410241024
CellA=B=C: 1648.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.611.611.61
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z1648.6401648.6401648.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-512-512-512
NC/NR/NS102410241024
D min/max/mean-0.0210.033-0.000

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Supplemental data

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Sample components

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Entire : Suid herpesvirus 1 (strain Becker)

EntireName: Suid herpesvirus 1 (strain Becker)
Components
  • Virus: Suid herpesvirus 1 (strain Becker)

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Supramolecule #1: Suid herpesvirus 1 (strain Becker)

SupramoleculeName: Suid herpesvirus 1 (strain Becker) / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10346 / Sci species name: Suid herpesvirus 1 (strain Becker) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Sus scrofa (pig)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1250.0 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
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-25 / Number real images: 1830 / Average electron dose: 18.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13537
CTF correctionSoftware: (Name: CTFFIND (ver. 3), RELION)
Startup modelType of model: INSILICO MODEL
In silico model: The particles were processed using EMAN for initial 3D reconstruction and refinement with icosahedral symmetry enforced.
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 13537
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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