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- EMDB-7047: CryoEM structure and atomic model of the Kaposi's sarcoma-associa... -

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Basic information

Entry
Database: EMDB / ID: 7047
TitleCryoEM structure and atomic model of the Kaposi's sarcoma-associated herpesvirus capsid
Map dataCryoEM structure and atomic model of the Kaposi's sarcoma-associated herpesvirus capsid
SampleHuman herpesvirus 8Herpesviridae:
virus / Major capsid protein / Small capsomere-interacting protein / (Triplex capsid protein ...) x 2
Function / homologyGammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus major capsid protein / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus VP23 like capsid protein / Herpes virus major capsid protein / Herpesvirus capsid shell protein VP19C / T=16 icosahedral viral capsid ...Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus major capsid protein / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus VP23 like capsid protein / Herpes virus major capsid protein / Herpesvirus capsid shell protein VP19C / T=16 icosahedral viral capsid / viral capsid assembly / viral capsid / host cell nucleus / viral process / structural molecule activity / DNA binding / Triplex capsid protein 2 / Major capsid protein / Small capsomere-interacting protein / Triplex capsid protein 1
Function and homology information
SourceHuman herpesvirus 8 / HHV-8 (virus)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsDai XH / Gong DY / Sun R / Zhou ZH
CitationJournal: Nature / Year: 2018
Title: Structure and mutagenesis reveal essential capsid protein interactions for KSHV replication.
Authors: Xinghong Dai / Danyang Gong / Hanyoung Lim / Jonathan Jih / Ting-Ting Wu / Ren Sun / Z Hong Zhou
Validation ReportPDB-ID: 6b43

SummaryFull reportAbout validation report
DateDeposition: Sep 25, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Apr 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6b43
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6b43
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7047.map.gz (map file in CCP4 format, 8388609 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1280 pix
1.03 Å/pix.
= 1318.4 Å
1280 pix
1.03 Å/pix.
= 1318.4 Å
1280 pix
1.03 Å/pix.
= 1318.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-11.596477500000001 - 15.720491000000001
Average (Standard dev.)0.008491504 (1.0703465)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128012801280
Origin-640.0-640.0-640.0
Limit639.0639.0639.0
Spacing128012801280
CellA=B=C: 1318.3999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z128012801280
origin x/y/z0.0000.0000.000
length x/y/z1318.4001318.4001318.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-640-640-640
NC/NR/NS128012801280
D min/max/mean-11.59615.7200.008

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Supplemental data

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Sample components

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Entire Human herpesvirus 8

EntireName: Human herpesvirus 8
Details: KSHV lytic replication was induced in an iSLK-puro cell line harboring the KSHV-BAC16 plasmid.
Number of components: 5

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Component #1: virus, Human herpesvirus 8

VirusName: Human herpesvirus 8Herpesviridae / Class: VIRION
Details: KSHV lytic replication was induced in an iSLK-puro cell line harboring the KSHV-BAC16 plasmid.
Empty: No / Enveloped: Yes / Isolate: STRAIN
MassTheoretical: 200 MDa
SpeciesSpecies: Human herpesvirus 8 / Strain: JSC-1
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: capsid / Diameter: 1300.0 Å / T number(triangulation number): 16

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Component #2: protein, Major capsid protein

ProteinName: Major capsid protein / Details: Coded by gene ORF25. / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 153.574188 kDa
SourceSpecies: HHV-8 (virus)

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Component #3: protein, Small capsomere-interacting protein

ProteinName: Small capsomere-interacting protein / Details: Coded by gene ORF65. / Number of Copies: 15 / Recombinant expression: No
MassTheoretical: 18.597824 kDa
SourceSpecies: HHV-8 (virus)

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Component #4: protein, Triplex capsid protein 1

ProteinName: Triplex capsid protein 1
Details: Coded by gene ORF62. It is the monomer in the heterotrimeric triplex structure.
Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 36.37484 kDa
SourceSpecies: HHV-8 (virus)

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Component #5: protein, Triplex capsid protein 2

ProteinName: Triplex capsid protein 2
Details: Coded by gene ORF26. Forms the dimer in the heterotrimeric triplex structure.
Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 34.278473 kDa
SourceSpecies: HHV-8 (virus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K
Details: The sample was manually blotted and frozen with a homemade plunger..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 14000.0 X (nominal), 24271.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 79.0 - K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 8007 / Sampling size: 2.5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 25315
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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