7T7I

EBV nuclear egress complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.97 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The nuclear egress complex of Epstein-Barr virus buds membranes through an oligomerization-driven mechanism.

Thorsen, M.K.Draganova, E.B.Heldwein, E.E.

(2022) PLoS Pathog 18: e1010623-e1010623

  • DOI: https://doi.org/10.1371/journal.ppat.1010623
  • Primary Citation of Related Structures:  
    7T7I

  • PubMed Abstract: 

    During replication, herpesviral capsids are translocated from the nucleus into the cytoplasm by an unusual mechanism, termed nuclear egress, that involves capsid budding at the inner nuclear membrane. This process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid. Although the NEC is essential for capsid nuclear egress across all three subfamilies of the Herpesviridae, most studies to date have focused on the NEC homologs from alpha- and beta- but not gammaherpesviruses. Here, we report the crystal structure of the NEC from Epstein-Barr virus (EBV), a prototypical gammaherpesvirus. The structure resembles known structures of NEC homologs yet is conformationally dynamic. We also show that purified, recombinant EBV NEC buds synthetic membranes in vitro and forms membrane-bound coats of unknown geometry. However, unlike other NEC homologs, EBV NEC forms dimers in the crystals instead of hexamers. The dimeric interfaces observed in the EBV NEC crystals are similar to the hexameric interfaces observed in other NEC homologs. Moreover, mutations engineered to disrupt the dimeric interface reduce budding. Putting together these data, we propose that EBV NEC-mediated budding is driven by oligomerization into membrane-bound coats.


  • Organizational Affiliation

    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear egress protein 2
A, C, E, G, I
200Human herpesvirus 4 strain B95-8Mutation(s): 0 
Gene Names: NEC2BFRF1
UniProt
Find proteins for P03185 (Epstein-Barr virus (strain B95-8))
Explore P03185 
Go to UniProtKB:  P03185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03185
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear egress protein 1
B, D, F, H, J
257Human herpesvirus 4 strain B95-8Mutation(s): 0 
Gene Names: NEC1BFLF2
UniProt
Find proteins for P0CK47 (Epstein-Barr virus (strain B95-8))
Explore P0CK47 
Go to UniProtKB:  P0CK47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CK47
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.97 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 238.153α = 90
b = 238.153β = 90
c = 137.532γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesNIH089

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references