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- PDB-6pph: Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex ... -

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Basic information

Entry
Database: PDB / ID: 6pph
TitleKaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-binding structure
Components
  • (Capsid vertex component ...) x 2
  • (Triplex capsid protein ...) x 2
  • Large tegument protein deneddylase
  • Major capsid protein
  • Small capsomere-interacting protein
KeywordsVIRAL PROTEIN / capsid / tegument / vertex / complex / VIRUS
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / DNA packaging / modulation by virus of host protein ubiquitination / viral release from host cell / viral genome packaging / thiol-dependent ubiquitinyl hydrolase activity / ubiquitinyl hydrolase 1 / Hydrolases, Acting on peptide bonds (peptidases), Cysteine endopeptidases ...T=16 icosahedral viral capsid / viral tegument / viral capsid assembly / DNA packaging / modulation by virus of host protein ubiquitination / viral release from host cell / viral genome packaging / thiol-dependent ubiquitinyl hydrolase activity / ubiquitinyl hydrolase 1 / Hydrolases, Acting on peptide bonds (peptidases), Cysteine endopeptidases / viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / host cell nucleus / viral process / structural molecule activity / DNA binding
Herpesvirus capsid shell protein 1 / Large tegument protein deneddylase / Gammaherpesvirus capsid / Herpesvirus capsid vertex component 1 / Herpesvirus large tegument protein, USP domain / Papain-like cysteine peptidase superfamily / Herpesvirus capsid protein 2 / Herpesvirus UL25 / Herpesvirus major capsid protein / Herpesvirus UL25 family ...Herpesvirus capsid shell protein 1 / Large tegument protein deneddylase / Gammaherpesvirus capsid / Herpesvirus capsid vertex component 1 / Herpesvirus large tegument protein, USP domain / Papain-like cysteine peptidase superfamily / Herpesvirus capsid protein 2 / Herpesvirus UL25 / Herpesvirus major capsid protein / Herpesvirus UL25 family / Herpesvirus VP23 like capsid protein / Herpes virus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpesvirus capsid shell protein VP19C / Herpesvirus UL17 protein / Herpesvirus tegument protein, N-terminal conserved region / Gammaherpesvirus capsid protein / Herpesvirus tegument ubiquitin-specific protease (htUSP) domain profile.
Triplex capsid protein 2 / Major capsid protein / Large tegument protein deneddylase / Small capsomere-interacting protein / Triplex capsid protein 1 / Capsid vertex component 1 / Capsid vertex component 2
Biological speciesHuman herpesvirus 8
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGong, D. / Dai, X. / Jih, J. / Liu, Y.T. / Bi, G.Q. / Sun, R. / Zhou, Z.H.
Funding support United States, China, 14items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM071940 United States
National Institutes of Health/National Institute of Dental and Craniofacial ResearchDE025567 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 ResearchDE027901 United States
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI094386 United States
National Institutes of Health/National Cancer InstituteCA177322 United States
National Institutes of Health/National Cancer InstituteCA091791 United States
National Institutes of Health/National Institute of Dental and Craniofacial ResearchDE023591 United States
Other government2017YFA0505300 China
Other government2016YFA0400900 China
National Institutes of Health/National Center for Research Resources1S10RR23057 United States
National Institutes of Health/National Institute of General Medical Sciences1U24GM116792 United States
National Science Foundation (United States)DBI-1338135 United States
National Science Foundation (United States)DMR-1548924 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 Report
SummaryFull reportAbout validation report
History
DepositionJul 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
k: Capsid vertex component 1
l: Capsid vertex component 2
m: Capsid vertex component 2
n: Large tegument protein deneddylase
o: Large tegument protein deneddylase
5: Triplex capsid protein 1
6: Triplex capsid protein 2
7: Triplex capsid protein 2
b: Triplex capsid protein 1
c: Triplex capsid protein 2
d: Triplex capsid protein 2
4: Major capsid protein
A: Small capsomere-interacting protein
2: Small capsomere-interacting protein
S: Major capsid protein
3: Small capsomere-interacting protein
T: Major capsid protein
1: Small capsomere-interacting protein
X: Major capsid protein
0: Small capsomere-interacting protein
W: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)1,823,34921
Polymers1,823,34921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, CATC-binding penton vertex registers can exist at all capsid vertices.
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TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Capsid vertex component ... , 2 types, 3 molecules klm

#1: Protein/peptide Capsid vertex component 1


Mass: 49586.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 8 / Strain: GK18 / References: UniProt: Q76RH8
#2: Protein/peptide Capsid vertex component 2


Mass: 61494.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 8 / Strain: GK18 / References: UniProt: Q76RI7

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Protein/peptide , 3 types, 12 molecules no4STXWA2310

#3: Protein/peptide Large tegument protein deneddylase


Mass: 290024.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 8 / Strain: GK18
References: UniProt: Q2HR64, ubiquitinyl hydrolase 1, Hydrolases, Acting on peptide bonds (peptidases), Cysteine endopeptidases
#6: Protein/peptide
Major capsid protein / MCP


Mass: 153574.188 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 8 / Strain: GK18 / References: UniProt: D0UZN7
#7: Protein/peptide
Small capsomere-interacting protein


Mass: 18597.824 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 8 / Strain: GK18 / References: UniProt: Q76RF4

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Triplex capsid protein ... , 2 types, 6 molecules 5b67cd

#4: Protein/peptide Triplex capsid protein 1


Mass: 36374.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 8 / Strain: GK18 / References: UniProt: Q76RF6
#5: Protein/peptide
Triplex capsid protein 2


Mass: 34278.473 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Human herpesvirus 8 / Strain: GK18 / References: UniProt: C7E5A9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human gammaherpesvirus 8Kaposi's sarcoma-associated herpesvirus
Type: VIRUS / Entity ID: 1,2,3,4,5,6,7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Human gammaherpesvirus 8 / Strain: BAC16
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 1250 nm / Triangulation number (T number): 16
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Chamber 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 14000 X / Calibrated magnification: 24271 X / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 79 K
Image recordingAverage exposure time: 13 sec. / Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8007
Image scansSampling size: 2.5 µns / Width: 1440 / Height: 1440 / Movie frames/image: 26

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Processing

Software

Classification: refinement / Version: 1.13_2998 / NB:

Name
phenix.real_space_refine
PHENIX
EM software
IDNameVersionCategory
1ETHANparticle selection
2EMANparticle selection
3Leginonimage acquisition
5CTFFIND3CTF correction
6RELION2.1CTF correction
9Coot0.8.6.1model fitting
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
14RELION2.13D reconstruction
15PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 44328
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 928740 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 180.4 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.006675211
f_angle_d1.0141102212
f_chiral_restr0.056911555
f_plane_restr0.007113262
f_dihedral_angle_d7.182945334

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