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- EMDB-30155: Epstein-Barr virus, C12 portal dodecamer -

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Basic information

Entry
Database: EMDB / ID: EMD-30155
TitleEpstein-Barr virus, C12 portal dodecamer
Map data
Sample
  • Virus: Human gammaherpesvirus 4 (Epstein-Barr virus)
    • Protein or peptide: Portal protein
KeywordsEpstein-Barr virus / portal dodecomer / tegumented capsid / VIRAL PROTEIN
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / virion component / host cell cytoplasm / host cell nucleus / Portal protein
Function and homology information
Biological speciesEpstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8)) / Human gammaherpesvirus 4 (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsLi Z / Yu X / Zeng M
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900869 China
National Natural Science Foundation of China (NSFC)81830090 China
National Natural Science Foundation of China (NSFC)81702001 China
Ministry of Science and Technology (MoST, China)2017YFA0505600 China
Ministry of Science and Technology (MoST, China)2016YFA0502101 China
CitationJournal: Cell Res / Year: 2020
Title: CryoEM structure of the tegumented capsid of Epstein-Barr virus.
Authors: Zhihai Li / Xiao Zhang / Lili Dong / Jingjing Pang / Miao Xu / Qian Zhong / Mu-Sheng Zeng / Xuekui Yu /
Abstract: Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and has been shown to be closely associated with various malignancies. Here, we present a complete atomic model of EBV, ...Epstein-Barr virus (EBV) is the primary cause of infectious mononucleosis and has been shown to be closely associated with various malignancies. Here, we present a complete atomic model of EBV, including the icosahedral capsid, the dodecameric portal and the capsid-associated tegument complex (CATC). Our in situ portal from the tegumented capsid adopts a closed conformation with its channel valve holding the terminal viral DNA and with its crown region firmly engaged by three layers of ring-like dsDNA, which, together with the penton flexibility, effectively alleviates the capsid inner pressure placed on the portal cap. In contrast, the CATCs, through binding to the flexible penton vertices in a stoichiometric manner, accurately increase the inner capsid pressure to facilitate the pressure-driven genome delivery. Together, our results provide important insights into the mechanism by which the EBV capsid, portal, packaged genome and the CATCs coordinately achieve a pressure balance to simultaneously benefit both viral genome retention and ejection.
History
DepositionMar 25, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bqt
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bqt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30155.png

Downloads & links

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Map

FileDownload / File: emd_30155.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 168 pix.
= 220.08 Å		1.31 Å/pix.
x 168 pix.
= 220.08 Å		1.31 Å/pix.
x 168 pix.
= 220.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.011
Minimum - Maximum-0.029908461 - 0.047356777
Average (Standard dev.)0.00006795108 (±0.004278277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 220.07999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z220.080220.080220.080
α/β/γ90.00090.00090.000
start NX/NY/NZ212211153
NX/NY/NZ80102186
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0300.0470.000

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Supplemental data

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Sample components

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Entire : Human gammaherpesvirus 4

EntireName: Human gammaherpesvirus 4 (Epstein-Barr virus)
Components
  • Virus: Human gammaherpesvirus 4 (Epstein-Barr virus)
    • Protein or peptide: Portal protein

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Supramolecule #1: Human gammaherpesvirus 4

SupramoleculeName: Human gammaherpesvirus 4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10376 / Sci species name: Human gammaherpesvirus 4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8
Molecular weightTheoretical: 68.539641 KDa
SequenceString: MFNMNVDESA SGALGSSAIP VHPTPASVRL FEILQGKYAY VQGQTIYANL RNPGVFSRQV FTHLFKRAIS HCTYDDVLHD WNKFEACIQ KRWPSDDSCA SRFRESTFES WSTTMKLTVR DLLTTNIYRV LHSRSVLSYE RYVDWICATG MVPAVKKPIT Q ELHSKIKS ...String:
MFNMNVDESA SGALGSSAIP VHPTPASVRL FEILQGKYAY VQGQTIYANL RNPGVFSRQV FTHLFKRAIS HCTYDDVLHD WNKFEACIQ KRWPSDDSCA SRFRESTFES WSTTMKLTVR DLLTTNIYRV LHSRSVLSYE RYVDWICATG MVPAVKKPIT Q ELHSKIKS LRDRCVCREL GHERTIRSIG TELYEATKEI IESLNSTFIP QFTEVTIEYL PRSDEYVAYY CGRRIRLHVL FP PAIFAGT VTFDSPVQRL YQNIFMCYRT LEHAKICQLL NTAPLKAIVG HGGRDMYKDI LAHLEQNSQR KDPKKELLNL LVK LSENKT ISGVTDVVEE FITDASNNLV DRNRLFGQPG ETAAQGLKKK VSNTVVKCLT DQINEQFDQI NGLEKERELY LKKI RSMES QLQASLGPGG NNPAASAPAA VAAEAASVDI LTGSTASAIE KLFNSPSASL GARVSGHNES ILNSFVSQYI PPSRE MTKD LTELWESELF NTFKLTPVVD NQGQRLYVRY SSDTISILLG PFTYLVAELS PVELVTDVYA TLGIVEIIDE LYRSSR LAI YIEDLGRKYC PASATGGDHG IRQAPSARGD TEPDHAKSKP ARDPPPGAGS

UniProtKB: Portal protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #0 - Average electron dose: 48.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 QUANTUM (4k x 4k) / #1 - Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 22782
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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