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- EMDB-1320: Direct visualization of the putative portal in the Kaposi's sarco... -

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Basic information

Entry
Database: EMDB / ID: EMD-1320
TitleDirect visualization of the putative portal in the Kaposi's sarcoma-associated herpesvirus capsid by cryoelectron tomography.
Map dataThis is a MRC density map averaged from KSHV A-capsid tomograms. 5-fold symmetry is applied along the unique vertex.
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 Virol / Year: 2007
Title: Direct visualization of the putative portal in the Kaposi's sarcoma-associated herpesvirus capsid by cryoelectron tomography.
Authors: Binbin Deng / Christine M O'Connor / Dean H Kedes / Z Hong Zhou /
Abstract: Genetic and biochemical studies have suggested the existence of a bacteriophage-like, DNA-packaging/ejecting portal complex in herpesviruses capsids, but its arrangement remained unknown. Here, we ...Genetic and biochemical studies have suggested the existence of a bacteriophage-like, DNA-packaging/ejecting portal complex in herpesviruses capsids, but its arrangement remained unknown. Here, we report the first visualization of a unique vertex in the Kaposi's sarcoma-associated herpesvirus (KSHV) capsid by cryoelectron tomography, thus providing direct structural evidence for the existence of a portal complex in a gammaherpesvirus. This putative KSHV portal is an internally localized, umbilicated structure and lacks all of the external machineries characteristic of portals in DNA bacteriophages.
History
DepositionJan 22, 2007-
Header (metadata) releaseFeb 5, 2007-
Map releaseJun 12, 2007-
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: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1320.gif

emd_1320.tif

emd_1320_1.tif

emd_1320_2.tif

emd_1320_3.tif

Downloads & links

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Map

FileDownload / File: emd_1320.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a MRC density map averaged from KSHV A-capsid tomograms. 5-fold symmetry is applied along the unique vertex.
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: 2.47 / Movie #1: 1.5
Minimum - Maximum-2.84971 - 4.91305
Average (Standard dev.)0.0705704 (±1.05499)
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-150-150-149
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-2.8504.9130.071

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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: Kaposis sarcoma-associated herpesvirus / NCBI-ID: 37296 / Sci species name: Human herpesvirus 8 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Kaposis sarcoma-associated herpesvirus
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 / Resolution method: OTHER / Software - Name: PROJALIGN

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