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- EMDB-10010: Atomic structure of the Epstein-Barr portal, structure I -

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Basic information

Entry
Database: EMDB / ID: EMD-10010
TitleAtomic structure of the Epstein-Barr portal, structure I
Map data
Sample
  • Complex: DNA packaging viral protein
    • Protein or peptide: Portal protein
Keywordsviral protein / DNA packaging
Function / homologyHerpesvirus portal protein / Herpesvirus UL6 like / chromosome organization / virion component / host cell nucleus / BBRF1 / Portal protein
Function and homology information
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus) / Epstein-Barr virus (strain GD1) (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsMachon C / Fabrega-Ferrer M
Funding support Spain, 7 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessRYC-2011-09071 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBFU 2014-54181 Spain
Spanish Ministry of Science, Innovation, and UniversitiesBPF2014-53550-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
Spanish Ministry of Science, Innovation, and UniversitiesSEV-2013-0347 Spain
European Commission653706
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
CitationJournal: Nat Commun / Year: 2019
Title: Atomic structure of the Epstein-Barr virus portal.
Authors: Cristina Machón / Montserrat Fàbrega-Ferrer / Daming Zhou / Ana Cuervo / José L Carrascosa / David I Stuart / Miquel Coll /
Abstract: Herpesviridae is a vast family of enveloped DNA viruses that includes eight distinct human pathogens, responsible for diseases that range from almost asymptomatic to severe and life-threatening. ...Herpesviridae is a vast family of enveloped DNA viruses that includes eight distinct human pathogens, responsible for diseases that range from almost asymptomatic to severe and life-threatening. Epstein-Barr virus infects B-cells and epithelial cells, causing infectious mononucleosis, as well as a number of cancers. Epstein-Barr infection cannot be cured since neither vaccine nor antiviral drug treatments are available. All herpesviruses contain a linear double-stranded DNA genome, enclosed within an icosahedral capsid. Viral portal protein plays a key role in the procapsid assembly and DNA packaging. The portal is the entrance and exit pore for the viral genome, making it an attractive pharmacological target for the development of new antivirals. Here we present the atomic structure of the portal protein of Epstein-Barr virus, solved by cryo-electron microscopy at 3.5 Å resolution. The detailed architecture of this protein suggests that it plays a functional role in DNA retention during packaging.
History
DepositionMay 31, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseSep 18, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rvr
  • Surface level: 0.0229
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10010.png

Downloads & links

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Map

FileDownload / File: emd_10010.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 220 pix.
= 242. Å		1.1 Å/pix.
x 220 pix.
= 242. Å		1.1 Å/pix.
x 220 pix.
= 242. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0229 / Movie #1: 0.0229
Minimum - Maximum-0.05884046 - 0.12890957
Average (Standard dev.)0.001016252 (±0.005942787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 242.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z242.000242.000242.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0590.1290.001

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Supplemental data

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Sample components

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Entire : DNA packaging viral protein

EntireName: DNA packaging viral protein
Components
  • Complex: DNA packaging viral protein
    • Protein or peptide: Portal protein

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Supramolecule #1: DNA packaging viral protein

SupramoleculeName: DNA packaging viral protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)

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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 GD1) (Epstein-Barr virus)
Strain: GD1
Molecular weightTheoretical: 68.539641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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: BBRF1

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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: 8
Component:
ConcentrationName
50.0 mMTris-HCl
20.0 mM2-mercaptoethanol
500.0 mMNaCl
1.0 mMEDTA
0.05 % w/vn-Dodecyl-B-D-Maltoside
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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