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- EMDB-20436: Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20436
TitleKaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-binding structure
Map data
SampleHuman gammaherpesvirus 8:
virus / (Capsid vertex component ...) x 2 / Large tegument protein deneddylase / (Triplex capsid protein ...) x 2 / Major capsid protein / Small capsomere-interacting protein
Function / homology
Function and homology information


T=16 icosahedral viral capsid / icosahedral viral capsid / viral tegument / viral capsid assembly / DNA packaging / viral release from host cell / viral genome packaging / modulation by virus of host protein ubiquitination / go:0036459: / ubiquitinyl hydrolase 1 ...T=16 icosahedral viral capsid / icosahedral viral capsid / viral tegument / viral capsid assembly / DNA packaging / viral release from host cell / viral genome packaging / modulation by virus of host protein ubiquitination / go:0036459: / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / virion / viral capsid / viral penetration into host nucleus / host cell cytoplasm / viral entry into host cell / viral envelope / structural molecule activity / viral process / host cell nucleus / DNA binding
Herpesvirus major capsid protein / Gammaherpesvirus capsid / Herpesvirus capsid shell protein 1 / Herpesvirus UL25 / Herpesvirus capsid vertex component 1 / Herpesvirus large tegument protein, USP domain / Herpesvirus major capsid protein, upper domain superfamily / Large tegument protein deneddylase / Papain-like cysteine peptidase superfamily / Herpesvirus capsid protein 2
Major capsid protein / Capsid vertex component 1 / Triplex capsid protein 1 / Small capsomere-interacting protein / Capsid vertex component 2 / Triplex capsid protein 2 / Large tegument protein deneddylase / Small capsomere-interacting protein / Capsid vertex component 1 / Triplex capsid protein 1 ...Major capsid protein / Capsid vertex component 1 / Triplex capsid protein 1 / Small capsomere-interacting protein / Capsid vertex component 2 / Triplex capsid protein 2 / Large tegument protein deneddylase / Small capsomere-interacting protein / Capsid vertex component 1 / Triplex capsid protein 1 / Major capsid protein / Capsid vertex component 2
Biological speciesHuman gammaherpesvirus 8 / HHV-8 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 Resources (NIH/NCRR)1S10RR23057 United States
Other government2016YFA0400900 China
National Science Foundation (NSF, United States)DBI-1338135 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028583 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE025567 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE027901 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA091791 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA177322 United States
Other government2017YFA0505300 China
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE023591 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: 6pph

SummaryFull reportAbout validation report
History
DepositionJul 6, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseSep 11, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pph
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6pph
  • 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_20436.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: 0.022 / Movie #1: 0.022
Minimum - Maximum0 - 1
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-0.0850.1350.005

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Supplemental data

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Segmentation: #1

Fileemd_20436_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: None

Fileemd_20436_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: None

Fileemd_20436_half_map_2.map
AnnotationNone
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: 8

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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, Capsid vertex component 1

ProteinName: Capsid vertex component 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.586555 kDa
SourceSpecies: HHV-8 (virus) / Strain: GK18

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Component #3: protein, Capsid vertex component 2

ProteinName: Capsid vertex component 2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 61.494383 kDa
SourceSpecies: HHV-8 (virus) / Strain: GK18

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Component #4: protein, Large tegument protein deneddylase

ProteinName: Large tegument protein deneddylase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 290.024844 kDa
SourceSpecies: HHV-8 (virus) / Strain: GK18

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Component #5: 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 #6: 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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Component #7: 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 #8: 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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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: 928740
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.8 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: 180.4
Output model

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