4OYD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

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
  • Structures With Same Primary Citation

  • 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

    Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptosis regulator BHRF1A, C158Epstein-barr virus strain ag876Mutation(s): 0 
Gene Names: BHRF1
Find proteins for P0C6Z1 (Epstein-Barr virus (strain AG876))
Explore P0C6Z1 
Go to UniProtKB:  P0C6Z1
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Computationally designed InhibitorB, D117synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.103α = 90
b = 113.869β = 90.03
c = 55.67γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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