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- PDB-6ppi: Kaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodeca... -

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Basic information

Entry
Database: PDB / ID: 6ppi
TitleKaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodecamer structure
ComponentsPortal protein
KeywordsVIRUS / portal / capsid / genome / genome packaging
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / chromosome organization => GO:0051276 / virion component => GO:0044423 / viral release from host cell / host cell nucleus / Portal protein / Portal protein
Function and homology information
Biological speciesHuman herpesvirus 8
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 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 Sciences (NIH/NIGMS)GM071940 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 Dental and Craniofacial Research (NIH/NIDCR)DE028583 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE027901 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094386 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA177322 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA091791 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE023591 United States
Other government2017YFA0505300 China
Other government2016YFA0400900 China
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1S10RR23057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, 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.
History
DepositionJul 7, 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
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • EMDB-20437
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein


Theoretical massNumber of molelcules
Total (without water)817,05012
Polymers817,05012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein


Mass: 68087.516 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: Subunit of portal complex present at KSHV's portal vertex; 12 copies constitute one dodecameric complex
Source: (natural) Human herpesvirus 8 / Strain: GK18 / References: UniProt: Q76RH0, UniProt: F5HGK9*PLUS

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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: all / 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 / Specimen holder 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 µm / Width: 1440 / Height: 1440 / Movie frames/image: 26

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.13_2998refinement
PHENIX1.13_2998refinement
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: C12 (12 fold cyclic)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39073 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 200 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003140380
ELECTRON MICROSCOPYf_angle_d0.679554852
ELECTRON MICROSCOPYf_chiral_restr0.04836336
ELECTRON MICROSCOPYf_plane_restr0.0066852
ELECTRON MICROSCOPYf_dihedral_angle_d3.533524204

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