4OYD

Crystal structure of a computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A computationally designed inhibitor of an epstein-barr viral bcl-2 protein induces apoptosis in infected cells.

Procko, E.Berguig, G.Y.Shen, B.W.Song, Y.Frayo, S.Convertine, A.J.Margineantu, D.Booth, G.Correia, B.E.Cheng, Y.Schief, W.R.Hockenbery, D.M.Press, O.W.Stoddard, B.L.Stayton, P.S.Baker, D.

(2014) Cell 157: 1644-1656

  • DOI: 10.1016/j.cell.2014.04.034

  • PubMed Abstract: 
  • Because apoptosis of infected cells can limit virus production and spread, some viruses have co-opted prosurvival genes from the host. This includes the Epstein-Barr virus (EBV) gene BHRF1, a homolog of human Bcl-2 proteins that block apoptosis and a ...

    Because apoptosis of infected cells can limit virus production and spread, some viruses have co-opted prosurvival genes from the host. This includes the Epstein-Barr virus (EBV) gene BHRF1, a homolog of human Bcl-2 proteins that block apoptosis and are associated with cancer. Computational design and experimental optimization were used to generate a novel protein called BINDI that binds BHRF1 with picomolar affinity. BINDI recognizes the hydrophobic cleft of BHRF1 in a manner similar to other Bcl-2 protein interactions but makes many additional contacts to achieve exceptional affinity and specificity. BINDI induces apoptosis in EBV-infected cancer lines, and when delivered with an antibody-targeted intracellular delivery carrier, BINDI suppressed tumor growth and extended survival in a xenograft disease model of EBV-positive human lymphoma. High-specificity-designed proteins that selectively kill target cells may provide an advantage over the toxic compounds used in current generation antibody-drug conjugates.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptosis regulator BHRF1
A, C
158Epstein-Barr virus (strain AG876)Mutation(s): 0 
Find proteins for P0C6Z1 (Epstein-Barr virus (strain AG876))
Go to UniProtKB:  P0C6Z1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Computationally designed Inhibitor
B, D
117N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.103α = 90.00
b = 113.869β = 90.03
c = 55.670γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy