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- EMDB-20433: Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20433
TitleKaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-absent structure
Map data
SampleHuman gammaherpesvirus 8:
virus / Small capsomere-interacting protein / Major capsid protein / (Triplex capsid protein ...) x 2
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral capsid / host cell nucleus / viral process / structural molecule activity / DNA binding
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
Triplex capsid protein 2 / Major capsid protein / Small capsomere-interacting protein / Triplex capsid protein 1
Biological speciesHuman gammaherpesvirus 8 / HHV-8 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGong D / Dai X / Jih J / Liu YT / Bi GQ / Sun R / Zhou ZH
Funding support United States, China, 14 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources1S10RR23057 United States
Other government2016YFA0400900 China
National Science Foundation (United States)DBI-1338135 United States
National Institutes of Health/National Institute of General Medical Sciences1U24GM116792 United States
National Science Foundation (United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical SciencesGM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial ResearchDE028583 United States
National Institutes of Health/National Institute of Dental and Craniofacial ResearchDE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI094386 United States
National Institutes of Health/National Institute of Dental and Craniofacial ResearchDE027901 United States
National Institutes of Health/National Cancer InstituteCA091791 United States
National Institutes of Health/National Cancer InstituteCA177322 United States
Other government2017YFA0505300 China
National Institutes of Health/National Institute of Dental and Craniofacial ResearchDE023591 United States
CitationJournal: Cell / Year: 2019
Title: DNA-Packing Portal and Capsid-Associated Tegument Complexes in the Tumor Herpesvirus KSHV.
Authors: Danyang Gong / Xinghong Dai / Jonathan Jih / Yun-Tao Liu / Guo-Qiang Bi / Ren Sun / Z Hong Zhou /
Abstract: Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes ...Assembly of Kaposi's sarcoma-associated herpesvirus (KSHV) begins at a bacteriophage-like portal complex that nucleates formation of an icosahedral capsid with capsid-associated tegument complexes (CATCs) and facilitates translocation of an ∼150-kb dsDNA genome, followed by acquisition of a pleomorphic tegument and envelope. Because of deviation from icosahedral symmetry, KSHV portal and tegument structures have largely been obscured in previous studies. Using symmetry-relaxed cryo-EM, we determined the in situ structure of the KSHV portal and its interactions with surrounding capsid proteins, CATCs, and the terminal end of KSHV's dsDNA genome. Our atomic models of the portal and capsid/CATC, together with visualization of CATCs' variable occupancy and alternate orientation of CATC-interacting vertex triplexes, suggest a mechanism whereby the portal orchestrates procapsid formation and asymmetric long-range determination of CATC attachment during DNA packaging prior to pleomorphic tegumentation/envelopment. Structure-based mutageneses confirm that a triplex deep binding groove for CATCs is a hotspot that holds promise for antiviral development.
Validation ReportPDB-ID: 6ppd

SummaryFull reportAbout validation report
History
DepositionJul 6, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseSep 11, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ppd
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ppd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20433.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 384 pix.
= 395.52 Å
1.03 Å/pix.
x 384 pix.
= 395.52 Å
1.03 Å/pix.
x 384 pix.
= 395.52 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 LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.031065535 (±0.17349486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z395.520395.520395.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0740.1170.003

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Supplemental data

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Mask #1

Fileemd_20433_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Human gammaherpesvirus 8

EntireName: Human gammaherpesvirus 8 / Number of components: 5

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Component #1: virus, Human gammaherpesvirus 8

VirusName: Human gammaherpesvirus 8Kaposi's sarcoma-associated herpesvirus
Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Human gammaherpesvirus 8 / Strain: BAC16
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16

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Component #2: protein, Small capsomere-interacting protein

ProteinName: Small capsomere-interacting protein / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 18.597824 kDa
SourceSpecies: HHV-8 (virus) / Strain: GK18

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Component #3: protein, Major capsid protein

ProteinName: Major capsid protein / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 153.574188 kDa
SourceSpecies: HHV-8 (virus) / Strain: GK18

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Component #4: protein, Triplex capsid protein 1

ProteinName: Triplex capsid protein 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 36.37484 kDa
SourceSpecies: HHV-8 (virus) / Strain: GK18

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Component #5: protein, Triplex capsid protein 2

ProteinName: Triplex capsid protein 2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 34.278473 kDa
SourceSpecies: HHV-8 (virus) / Strain: GK18

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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
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: ( - 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 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1521505
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 177.4
Output model

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