3BIM

Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer.

Ghetu, A.F., Corcoran, C.M., Cerchietti, L., Bardwell, V.J., Melnick, A., Prive, G.G.

(2008) Mol Cell 29: 384-391

  • DOI: 10.1016/j.molcel.2007.12.026
  • Primary Citation of Related Structures:  
    3BIM

  • PubMed Abstract: 

    • The transcriptional corepressors BCOR, SMRT, and NCoR are known to bind competitively to the BCL6 BTB domain despite the fact that BCOR has no detectable sequence similarity to the other two corepressors. We have identified a 17 residue motif from BCOR t ...

    The transcriptional corepressors BCOR, SMRT, and NCoR are known to bind competitively to the BCL6 BTB domain despite the fact that BCOR has no detectable sequence similarity to the other two corepressors. We have identified a 17 residue motif from BCOR that binds directly to the BCL6 BTB domain and determined the crystal structure of the complex to a resolution of 2.6 A. Remarkably, the BCOR BCL6 binding domain (BCOR(BBD)) peptide binds in the same BCL6 binding site as the SMRT(BBD) peptide despite the lack of any significant sequence similarity between the two peptides. Mutations of critical BCOR(BBD) residues cause the disruption of the BCL6 corepression activities of BCOR, and a BCOR(BBD) peptide blocks BCL6-mediated transcriptional repression and kills lymphoma cells.

    Organizational Affiliation: 

    Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, 101 College Street, Toronto, ON M5G 1L7, Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein A, B, C, D, E, F, G, H127Homo sapiensMutation(s): 3 
Gene Names: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
NIH Common Fund Data Resources
PHAROS:  P41182
GTEx:  ENSG00000113916
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BCL-6 corepressor I, J, K, L, M, N, O, P19Homo sapiensMutation(s): 0 
Gene Names: BCOR, KIAA1575
Find proteins for Q6W2J9 (Homo sapiens)
Explore Q6W2J9 
Go to UniProtKB:  Q6W2J9
NIH Common Fund Data Resources
PHAROS:  Q6W2J9
GTEx:  ENSG00000183337
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.55α = 90
b = 150.55β = 90
c = 312.25γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description