|Entry||Database: EMDB / ID: EMD-10010|
|Title||Atomic structure of the Epstein-Barr portal, structure I|
|Sample||DNA packaging viral protein:|
|Function / homology||Herpesvirus portal protein / Herpesvirus UL6 like / DNA packaging / viral release from host cell / virion / host cell nucleus / Portal protein|
Function and homology information
|Biological species||Human gammaherpesvirus 4 (Epstein-Barr virus) / Epstein-Barr virus (strain GD1) (Epstein-Barr virus)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.46 Å|
|Authors||Machon C / Fabrega-Ferrer M / Zhou D / Cuervo A / Carrascosa JL / Stuart DI / Coll M|
|Funding support|| Spain, 7 items |
|Citation||Journal: 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.
|Validation Report||PDB-ID: 6rvr|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_10010.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.1 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire DNA packaging viral protein
|Entire||Name: DNA packaging viral protein / Number of components: 2|
-Component #1: protein, DNA packaging viral protein
|Protein||Name: DNA packaging viral protein / Recombinant expression: No|
|Source||Species: Human gammaherpesvirus 4 (Epstein-Barr virus)|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm) / Cell of expression system: Sf9 cell line|
-Component #2: protein, Portal protein
|Protein||Name: Portal protein / Number of Copies: 12 / Recombinant expression: No|
|Mass||Theoretical: 68.539641 kDa|
|Source||Species: Epstein-Barr virus (strain GD1) (Epstein-Barr virus)|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 44 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C12 (12 fold cyclic) / Number of projections: 73395|
|3D reconstruction||Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF|
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