[English] 日本語
Yorodumi
- EMDB-20433: Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20433
TitleKaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-absent structure
Map dataNone
Sample
  • Virus: Human gammaherpesvirus 8
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2
Function / homology
Function and homology information


T=16 icosahedral viral capsid / viral capsid assembly / viral process / viral capsid / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Gammaherpesvirus capsid / Gammaherpesvirus capsid protein / Herpesvirus capsid protein 2 / Herpesvirus capsid shell protein 1 / Herpesvirus VP23 like capsid protein / Herpesvirus capsid shell protein VP19C / Herpesvirus major capsid protein / Herpesvirus major capsid protein, upper domain superfamily / Herpes virus major capsid protein
Similarity search - Domain/homology
Triplex capsid protein 2 / Major capsid protein / Triplex capsid protein 1 / Small capsomere-interacting protein / Major capsid protein / Small capsomere-interacting protein / Triplex capsid protein 1
Similarity search - Component
Biological speciesHHV-8 (virus) / Human gammaherpesvirus 8
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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 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.
History
DepositionJul 6, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseSep 11, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ppd
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ppd
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_20433.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.073839344 - 0.11739924
Average (Standard dev.)0.003356943 (±0.0077708424)
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-0.0740.1170.003

-
Supplemental data

-
Mask #1

Fileemd_20433_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: None

Fileemd_20433_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: None

Fileemd_20433_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : Human gammaherpesvirus 8

EntireName: Human gammaherpesvirus 8
Components
  • Virus: Human gammaherpesvirus 8
    • Protein or peptide: Small capsomere-interacting protein
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Triplex capsid protein 1
    • Protein or peptide: Triplex capsid protein 2

-
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: Small capsomere-interacting protein

MacromoleculeName: Small capsomere-interacting protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: HHV-8 (virus) / Strain: GK18
Molecular weightTheoretical: 18.597824 KDa
SequenceString:
MSNFKVRDPV IQERLDHDYA HHPLVARMNT LDQGNMSQAE YLVQKRHYLV FLIAHHYYEA YLRRMGGIQR RDHLQTLRDQ KPRERADRV SAASAYDAGT FTVPSRPGPA SGTTPGGQDS LGVSGSSITT LSSGPHSLSP ASDILTTLSS TTETAAPAVA D ARKPPSGK KK

-
Macromolecule #2: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: HHV-8 (virus) / Strain: GK18
Molecular weightTheoretical: 153.574188 KDa
SequenceString: MEATLEQRPF PYLATEANLL TQIKESAADG LFKSFQLLLG KDAREGSVRF EALLGVYTNV VEFVKFLETA LAAACVNTEF KDLRRMIDG KIQFKISMPT IAHGDGRRPN KQRQYIVMKA CNKHHIGAEI ELAAADIELL FAEKETPLDF TEYAGAIKTI T SALQFGMD ...String:
MEATLEQRPF PYLATEANLL TQIKESAADG LFKSFQLLLG KDAREGSVRF EALLGVYTNV VEFVKFLETA LAAACVNTEF KDLRRMIDG KIQFKISMPT IAHGDGRRPN KQRQYIVMKA CNKHHIGAEI ELAAADIELL FAEKETPLDF TEYAGAIKTI T SALQFGMD ALERGLVDTV LAVKLRHAPP VFILKTLGDP VYSERGLKKA VKSDMVSMFK AHLIEHSFFL DKAELMTRGK QY VLTMLSD MLAAVCEDTV FKGVSTYTTA SGQQVAGVLE TTDSVMRRLM NLLGQVESAM SGPAAYASYV VRGANLVTAV SYG RAMRNF EQFMARIVDH PNALPSVEGD KAALADGHDE IQRTRIAASL VKIGDKFVAI ESLQRMYNET QFPCPLNRRI QYTY FFPVG LHLPVPRYST SVSVRGVESP AIQSTETWVV NKNNVPLCFG YQNALKSICH PRMHNPTQSA QALNQAFPDP DGGHG YGLR YEQTPNMNLF RTFHQYYMGK NVAFVPDVAQ KALVTTEDLL HPTSHRLLRL EVHPFFDFFV HPCPGARGSY RATHRT MVG NIPQPLAPRE FQESRGAQFD AVTNMTHVID QLTIDVIQET AFDPAYPLFC YVIEAMIHGQ EEKFVMNMPL IALVIQT YW VNSGKLAFVN SYHMVRFICT HMGNGSIPKE AHGHYRKILG ELIALEQALL KLAGHETVGR TPITHLVSAL LDPHLLPP F AYHDVFTDLM QKSSRQPIIK IGDQNYDNPQ NRATFINLRG RMEDLVNNLV NIYQTRVNED HDERHVLDVA PLDENDYNP VLEKLFYYVL MPVCSNGHMC GMGVDYQNVA LTLTYNGPVF ADVVNAQDDI LLHLENGTLK DILQAGDIRP TVDMIRVLCT SFLTCPFVT QAARVITKRD PAQSFATHEY GKDVAQTVLV NGFGAFAVAD RSREAAETMF YPVPFNKLYA DPLVAATLHP L LANYVTRL PNQRNAVVFN VPSNLMAEYE EWHKSPVAAY AASCQATPGA ISAMVSMHQK LSAPSFICQA KHRMHPGFAM TV VRTDEVL AEHILYCSRA STSMFVGLPS VVRREVRSDA VTFEITHEIA SLHTALGYSS VIAPAHVAAI TTDMGVHCQD LFM IFPGDA YQDRQLHDYI KMKAGVQTGP PGNRMDHVGY AAGVPRCENL PGLSHGQLAT CEIIPTPVTS DVAYFQTPSN PRGR AACVV SCDAYSNESA ERLLYDHSIP DPAYECRSTN NPWASQRGSL GDVLYNITFR QTALPGMYSP CRQFFHKEDI MRYNR GLYT LVNEYSARLA GAPATSTTDL QYVVVNGTDV FLDQPCHMLQ EAYPTLAASH RVMLDEYMSN KQTHAPVHMG QYLIEE VAP MKRLLKLGNK VVY

-
Macromolecule #3: Triplex capsid protein 1

MacromoleculeName: Triplex capsid protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HHV-8 (virus) / Strain: GK18
Molecular weightTheoretical: 36.37484 KDa
SequenceString: MKVQAENAAR LGRQVLGLLP PPTHRVSLTR GPEFARGVRD LLSKYAASTR PTVGSLHEAL RQAPFRQPTY GDFLVYSQTF SPQEPLGTF LFSFKQEDNG SSMDMLLTPT SLFMLSGMEA AKAPQTHKVA GVWYGSGSGL ADFIPNLSEL MDTGEFHTLL T PVGPMVQS ...String:
MKVQAENAAR LGRQVLGLLP PPTHRVSLTR GPEFARGVRD LLSKYAASTR PTVGSLHEAL RQAPFRQPTY GDFLVYSQTF SPQEPLGTF LFSFKQEDNG SSMDMLLTPT SLFMLSGMEA AKAPQTHKVA GVWYGSGSGL ADFIPNLSEL MDTGEFHTLL T PVGPMVQS VHSTFVTKVT SAMKGVGLAR DEPRAHVGLT LPCDMLVDLD ESCPMVQRRE PAGLNVTIYA SLVYLRVNQR PS MALTFFQ SGKGFAEVVA MIKDHFTDVI RTKYIQLRHE LYINRLVFGA VCTLGTVPFD SHPVHQSLNV KGTSLPVLVF ANF EAACGP WTVFL

-
Macromolecule #4: Triplex capsid protein 2

MacromoleculeName: Triplex capsid protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: HHV-8 (virus) / Strain: GK18
Molecular weightTheoretical: 34.278473 KDa
SequenceString: MALDKSIVVN LTSRLFADEL AALQSKIGSV LPLGDCHRLQ NIQALGLGCV CSRETSPDYI QIMQYLSKCT LAVLEEVRPD SLRLTRMDP SDNLQIKNVY APFFQWDSNT QLAVLPPLFS RKDSTIVLES NGFDIVFPMV VPQQLGHAIL QQLLVYHIYS K ISAGAPGD ...String:
MALDKSIVVN LTSRLFADEL AALQSKIGSV LPLGDCHRLQ NIQALGLGCV CSRETSPDYI QIMQYLSKCT LAVLEEVRPD SLRLTRMDP SDNLQIKNVY APFFQWDSNT QLAVLPPLFS RKDSTIVLES NGFDIVFPMV VPQQLGHAIL QQLLVYHIYS K ISAGAPGD VNMAELDLYT TNVSFMGRTY RLDVDNTDPR TALRVLDDLS MYLCILSALV PRGCLRLLTA LVRHDRHPLT EV FEGVVPD EVTRIDLDQL SVPDDITRMR VMFSYLQSLS SIFNLGPRLH VYAYSAETLA ASCWYSPR

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
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 / Digitization - Sampling interval: 2.5 µm / 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
CTF correctionSoftware: (Name: CTFFIND (ver. 3.0), RELION (ver. 2.1))
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: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 1521505
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 177.4 / Target criteria: Correlation coefficient
Output model

PDB-6ppd:
Kaposi's sarcoma-associated herpesvirus (KSHV), C1 penton vertex register, CATC-absent 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