4Z3U

PRV nuclear egress complex

  • Classification: VIRAL PROTEIN
  • Organism(s): Suid alphaherpesvirus 1
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-03-31 Released: 2015-11-11 
  • Deposition Author(s): Bigalke, J.M., Heldwein, E.E.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Burroughs Wellcome Fund, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis of membrane budding by the nuclear egress complex of herpesviruses.

Bigalke, J.M.Heldwein, E.E.

(2015) EMBO J 34: 2921-2936

  • DOI: 10.15252/embj.201592359
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During nuclear egress, herpesvirus capsids bud at the inner nuclear membrane forming perinuclear viral particles that subsequently fuse with the outer nuclear membrane, releasing capsids into the cytoplasm. This unusual budding process is mediated by ...

    During nuclear egress, herpesvirus capsids bud at the inner nuclear membrane forming perinuclear viral particles that subsequently fuse with the outer nuclear membrane, releasing capsids into the cytoplasm. This unusual budding process is mediated by the nuclear egress complex (NEC) composed of two conserved viral proteins, UL31 and UL34. Earlier, we discovered that the herpesvirus nuclear egress complex (NEC) could bud synthetic membranes in vitro without the help of other proteins by forming a coat-like hexagonal scaffold inside the budding membrane. To understand the structural basis of NEC-mediated membrane budding, we determined the crystal structures of the NEC from two herpesviruses. The hexagonal lattice observed in the NEC crystals recapitulates the honeycomb coats within the budded vesicles. Perturbation of the oligomeric interfaces through mutagenesis blocks budding in vitro confirming that NEC oligomerization into a honeycomb lattice drives budding. The structure represents the first atomic-level view of an oligomeric array formed by a membrane-deforming protein, making possible the dissection of its unique budding mechanism and the design of inhibitors to block it.


    Organizational Affiliation

    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA katya.heldwein@tufts.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UL34 proteinA, C181Suid alphaherpesvirus 1Mutation(s): 0 
Gene Names: UL34NEC2
Find proteins for G3G8X8 (Suid alphaherpesvirus 1)
Explore G3G8X8 
Go to UniProtKB:  G3G8X8
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UL31B, D258Suid alphaherpesvirus 1Mutation(s): 0 
Gene Names: UL31NEC1
Find proteins for G3G955 (Suid alphaherpesvirus 1)
Explore G3G955 
Go to UniProtKB:  G3G955
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.217 
  • Space Group: P 43 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/188 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.456α = 90
b = 125.456β = 90
c = 109.235γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
PHENIXmodel building
SHELXphasing
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM111795-01
Burroughs Wellcome Fund--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R21AI097573-01A1
German Research Foundation (DFG)GermanyBI 1658/1-1

Revision History 

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.3: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.4: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence