5DOB

Crystal structure of the Human Cytomegalovirus Nuclear Egress Complex (NEC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.254 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unexpected features and mechanism of heterodimer formation of a herpesvirus nuclear egress complex.

Lye, M.F.Sharma, M.El Omari, K.Filman, D.J.Schuermann, J.P.Hogle, J.M.Coen, D.M.

(2015) Embo J. 34: 2937-2952

  • DOI: 10.15252/embj.201592651
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herpesvirus nucleocapsids escape from the nucleus in a process orchestrated by a highly conserved, viral nuclear egress complex. In human cytomegalovirus, the complex consists of two proteins, UL50 and UL53. We solved structures of versions of UL53 a ...

    Herpesvirus nucleocapsids escape from the nucleus in a process orchestrated by a highly conserved, viral nuclear egress complex. In human cytomegalovirus, the complex consists of two proteins, UL50 and UL53. We solved structures of versions of UL53 and the complex by X-ray crystallography. The UL53 structures, determined at 1.93 and 3.0 Å resolution, contained unexpected features including a Bergerat fold resembling that found in certain nucleotide-binding proteins, and a Cys3His zinc finger. Substitutions of zinc-coordinating residues decreased UL50-UL53 co-localization in transfected cells, and, when incorporated into the HCMV genome, ablated viral replication. The structure of the complex, determined at 2.47 Å resolution, revealed a mechanism of heterodimerization in which UL50 clamps onto helices of UL53 like a vise. Substitutions of particular residues on the interaction interface disrupted UL50-UL53 co-localization in transfected cells and abolished virus production. The structures and the identification of contacts can be harnessed toward the rational design of novel and highly specific antiviral drugs and will aid in the detailed understanding of nuclear egress.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Virion egress protein UL31 homolog
A
237Human cytomegalovirus (strain AD169)Mutation(s): 5 
Gene Names: NEC1
Find proteins for P16794 (Human cytomegalovirus (strain AD169))
Go to UniProtKB:  P16794
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Virion egress protein UL34 homolog
B
165Human cytomegalovirus (strain AD169)Mutation(s): 0 
Gene Names: NEC2
Find proteins for P16791 (Human cytomegalovirus (strain AD169))
Go to UniProtKB:  P16791
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.254 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.254α = 90.00
b = 33.978β = 121.76
c = 92.995γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI026077

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description