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- EMDB-1446: Cryo-electron tomography of Kaposi's sarcoma-associated herpesvir... -

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Basic information

Entry
Database: EMDB / ID: EMD-1446
TitleCryo-electron tomography of Kaposi's sarcoma-associated herpesvirus capsids reveals dynamic scaffolding structures essential to capsid assembly and maturation.
Map dataKSHV B capsid
Sample
  • Sample: KSHV
  • Virus: Human herpesvirus 8
Biological speciesHuman herpesvirus 8
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 Å
AuthorsDeng B / O'Connor CM / Kedes DH / Zhou ZH
CitationJournal: J Struct Biol / Year: 2008
Title: Cryo-electron tomography of Kaposi's sarcoma-associated herpesvirus capsids reveals dynamic scaffolding structures essential to capsid assembly and maturation.
Authors: Binbin Deng / Christine M O'Connor / Dean H Kedes / Z Hong Zhou /
Abstract: Kaposi's sarcoma-associated herpesvirus (KSHV) is a recently discovered DNA tumor virus that belongs to the gamma-herpesvirus subfamily. Though numerous studies on KSHV and other herpesviruses, in ...Kaposi's sarcoma-associated herpesvirus (KSHV) is a recently discovered DNA tumor virus that belongs to the gamma-herpesvirus subfamily. Though numerous studies on KSHV and other herpesviruses, in general, have revealed much about their multilayered organization and capsid structure, the herpesvirus capsid assembly and maturation pathway remains poorly understood. Structural variability or irregularity of the capsid internal scaffolding core and the lack of adequate tools to study such structures have presented major hurdles to earlier investigations employing more traditional cryo-electron microscopy (cryoEM) single particle reconstruction. In this study, we used cryo-electron tomography (cryoET) to obtain 3D reconstructions of individual KSHV capsids, allowing direct visualization of the capsid internal structures and systematic comparison of the scaffolding cores for the first time. We show that B-capsids are not a structurally homogenous group; rather, they represent an ensemble of "B-capsid-like" particles whose inner scaffolding is highly variable, possibly representing different intermediates existing during the KSHV capsid assembly and maturation. This information, taken together with previous observations, has allowed us to propose a detailed pathway of herpesvirus capsid assembly and maturation.
History
DepositionOct 23, 2007-
Header (metadata) releaseOct 25, 2007-
Map releaseOct 25, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1446.gif

Downloads & links

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Map

FileDownload / File: emd_1446.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKSHV B capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.86 Å/pix.
x 168 pix.
= 1320.144 Å		7.86 Å/pix.
x 168 pix.
= 1320.144 Å		7.86 Å/pix.
x 168 pix.
= 1320.144 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.858 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.32 / Movie #1: 1.2
Minimum - Maximum-9.94937 - 10.250999999999999
Average (Standard dev.)0.020808 (±1.22123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-84-84-84
Dimensions168168168
Spacing168168168
CellA=B=C: 1320.14 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.8587.8587.858
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z1320.1441320.1441320.144
α/β/γ90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-9.94910.2510.021

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Supplemental data

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Sample components

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Entire : KSHV

EntireName: KSHV
Components
  • Sample: KSHV
  • Virus: Human herpesvirus 8

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Supramolecule #1000: KSHV

SupramoleculeName: KSHV / type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 1

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Supramolecule #1: Human herpesvirus 8

SupramoleculeName: Human herpesvirus 8 / type: virus / ID: 1 / Name.synonym: Kaposi's sarcoma-associated herpesvirus, HHV8 / NCBI-ID: 37296 / Sci species name: Human herpesvirus 8 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Syn species name: Kaposi's sarcoma-associated herpesvirus, HHV8
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: PBS
GridDetails: holey carbon 300 mesh copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: Blot for 1 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
DetailsTilted from -70 to +70 with 2 degree interval.
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 23000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: 70 ° / Tilt series - Axis1 - Max angle: 70 °
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 40.0 Å / Software - Name: PROJALIGN

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