4CP3

The structure of BCL6 BTB (POZ) domain in complex with the ansamycin antibiotic rifabutin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Ansamycin Antibiotic, Rifamycin Sv, Inhibits Bcl6 Transcriptional Repression and Forms a Complex with the Bcl6-Btb/Poz Domain.

Evans, S.E.Goult, B.T.Fairall, L.Jamieson, A.G.Ko Ferrigno, P.Ford, R.Schwabe, J.W.R.Wagner, S.D.

(2014) Plos One 9: 90889

  • DOI: 10.1371/journal.pone.0090889

  • PubMed Abstract: 
  • BCL6 is a transcriptional repressor that is over-expressed due to chromosomal translocations, or other abnormalities, in ∼40% of diffuse large B-cell lymphoma. BCL6 interacts with co-repressor, SMRT, and this is essential for its role in lymphomas. P ...

    BCL6 is a transcriptional repressor that is over-expressed due to chromosomal translocations, or other abnormalities, in ∼40% of diffuse large B-cell lymphoma. BCL6 interacts with co-repressor, SMRT, and this is essential for its role in lymphomas. Peptide or small molecule inhibitors, which prevent the association of SMRT with BCL6, inhibit transcriptional repression and cause apoptosis of lymphoma cells in vitro and in vivo. In order to discover compounds, which have the potential to be developed into BCL6 inhibitors, we screened a natural product library. The ansamycin antibiotic, rifamycin SV, inhibited BCL6 transcriptional repression and NMR spectroscopy confirmed a direct interaction between rifamycin SV and BCL6. To further determine the characteristics of compounds binding to BCL6-POZ we analyzed four other members of this family and showed that rifabutin, bound most strongly. An X-ray crystal structure of the rifabutin-BCL6 complex revealed that rifabutin occupies a partly non-polar pocket making interactions with tyrosine58, asparagine21 and arginine24 of the BCL6-POZ domain. Importantly these residues are also important for the interaction of BLC6 with SMRT. This work demonstrates a unique approach to developing a structure activity relationship for a compound that will form the basis of a therapeutically useful BCL6 inhibitor.


    Organizational Affiliation

    Department of Biochemistry, University of Leicester, Leicester, United Kingdom; Department of Cancer Studies and Molecular Medicine and MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B-CELL LYMPHOMA 6 PROTEIN
A, B
124Homo sapiensMutation(s): 2 
Gene Names: BCL6 (BCL5, LAZ3, ZBTB27, ZNF51)
Find proteins for P41182 (Homo sapiens)
Go to Gene View: BCL6
Go to UniProtKB:  P41182
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBT
Query on RBT

Download SDF File 
Download CCD File 
B
RIFABUTIN
(9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6-16,18,20- TETRAHYDROXY-1'-ISOBUTYL-14-METHOXY-7,9,15,17,19,21,25- HEPTAMETHYLSPIRO(9,4-(EPOXYPENTADECA(1,11,13)TRIENIMINO)-2H- FURO(2',3':7,8)NAPHTH(1,2-D)IMIDAZOLE-2,4'-PIPERIDINE)- 5,10,26(3H,9H)-TRIONE,16-ACETATE; ANSAMYCIN
C46 H62 N4 O11
ATEBXHFBFRCZMA-VXTBVIBXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.172α = 90.00
b = 54.828β = 95.21
c = 58.159γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release