[English] 日本語
Yorodumi
- EMDB-20437: Kaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodeca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20437
TitleKaposi's sarcoma-associated herpesvirus (KSHV), C12 portal dodecamer structure
Map dataNone
Sample
  • Virus: Human gammaherpesvirus 8
    • Protein or peptide: Portal protein
Keywordsportal / capsid / genome / genome packaging / VIRUS
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 / Human gammaherpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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 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, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseSep 11, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ppi
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20437.png

Downloads & links

-
Map

FileDownload / File: emd_20437.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.0145 / Movie #1: 0.0145
Minimum - Maximum-0.021977358 - 0.037896827
Average (Standard dev.)0.0026665933 (±0.004151186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 197.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z197.760197.760197.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0220.0380.003

-
Supplemental data

-
Sample components

-
Entire : Human gammaherpesvirus 8

EntireName: Human gammaherpesvirus 8
Components
  • Virus: Human gammaherpesvirus 8
    • Protein or peptide: Portal protein

-
Supramolecule #1: Human gammaherpesvirus 8

SupramoleculeName: Human gammaherpesvirus 8 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 37296 / Sci species name: Human gammaherpesvirus 8 / Sci species strain: BAC16 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1250.0 Å / T number (triangulation number): 16

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1
Details: Subunit of portal complex present at KSHV's portal vertex; 12 copies constitute one dodecameric complex
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 8 / Strain: GK18
Molecular weightTheoretical: 68.087516 KDa
SequenceString: MLRMNPGLGS SISVHPSELS ISLFEILQGK YSYVRGQTLH CSLRNPGVFF RQLFIHLYKN ALANCSYDHV LSDWRTYESS AKTRWPEKE AQWGSYRRST FDSWAQTMRM TLDHLLLNAI NRVLYAKTQL SYERYVDWVV TVGMVPVVKH TPDHKLVNSI Q EQLMKDCQ ...String:
MLRMNPGLGS SISVHPSELS ISLFEILQGK YSYVRGQTLH CSLRNPGVFF RQLFIHLYKN ALANCSYDHV LSDWRTYESS AKTRWPEKE AQWGSYRRST FDSWAQTMRM TLDHLLLNAI NRVLYAKTQL SYERYVDWVV TVGMVPVVKH TPDHKLVNSI Q EQLMKDCQ RLASGEKTIG RILTSVTQEI SNLVSSLSAL YIPGYSEVSI DYDCVKNTFV GLYKQKRVHV EVITMPAILA GR VIFDSPI QRMYTSIMSC HRTAEHAKLC QLLNTAPTKA LVGSACNNVY KDIMTHLEQA SQRTDPKREL LNLLMKLAEN KTV SGVTDV VEDFVTDVSQ NIVDKNKLFG TGQETTTQGL RRQVSNSVFK CLTNQINEQF DTITQLEKER ELCMKRLKCI ETQL SHQQP GDAKGPGSVN LLTANTFQSL GRLQDPSLQL TSSHIPSGSA VLNSFFSSYI PPVRESMKDL TNLWESEMFQ TYKLA PVVD NQGQRLSVTY SQDTISILLG PFTYVIADLL QMELISHSFV SSSLQDIAAY LYQTSRLFVY ITDVGQKYCL VTPPFE NVP GKGPGETDWS ANEYSCPEDS RVRRGLSRIP PPCGAPPCPG SA

UniProtKB: Portal protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER
Details: The sample was manually blotted and frozen with a homemade plunger..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 24271 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 14000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMax: 79.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Dimensions - Width: 1440 pixel / Digitization - Dimensions - Height: 1440 pixel / Number real images: 8007 / Average exposure time: 13.0 sec. / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 44328
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 39073

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 200 / Target criteria: Correlation coefficient
Output model

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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