[English] 日本語
Yorodumi
- PDB-6ppi: Kaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodeca... -

+
Open data


ID or keywords:

Loading...

-
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 / DNA packaging / viral release from host cell / virion / host cell nucleus / 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 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 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20437
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein/peptide
Portal protein


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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Human gammaherpesvirus 8Kaposi's sarcoma-associated herpesvirus
Type: VIRUS / Entity ID: 1 / 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.

-
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

-
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: 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

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.003140380
f_angle_d0.679554852
f_chiral_restr0.04836336
f_plane_restr0.0066852
f_dihedral_angle_d3.533524204

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more