Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.17 kDa 
• Atom Count: 2405 
• Modelled Residue Count: 284 
• Deposited Residue Count: 292 
• Unique protein chains: 2

1R2B

Crystal structure of the BCL6 BTB domain complexed with a SMRT co-repressor peptide

• PDB DOI: 10.2210/pdb1R2B/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-09-26 Released: 2003-12-23 
• Deposition Author(s): Ahmad, K.F., Melnick, A., Lax, S.A., Bouchard, D., Liu, J., Kiang, C.L., Mayer, S., Licht, J.D., Prive, G.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain.

Ahmad, K.F., Melnick, A., Lax, S., Bouchard, D., Liu, J., Kiang, C.L., Mayer, S., Takahashi, S., Licht, J.D., Prive, G.G.

(2003) Mol Cell 12: 1551-1564

• PubMed: 14690607 
• DOI: 10.1016/s1097-2765(03)00454-4
• Primary Citation of Related Structures:  
  1R28, 1R29, 1R2B


• PubMed Abstract: 
  

BCL6 encodes a transcription factor that represses genes necessary for the terminal differentiation of lymphocytes within germinal centers, and the misregulated expression of this factor is strongly implicated in several types of B cell lymphoma. The homodimeric BTB domain of BCL6 (also known as the POZ domain) is required for the repression activity of the protein and interacts directly with the SMRT and N-CoR corepressors that are found within large multiprotein histone deacetylase-containing complexes. We have identified a 17 residue fragment from SMRT that binds to the BCL6 BTB domain, and determined the crystal structure of the complex to 2.2 A. Two SMRT fragments bind symmetrically to the BCL6 BTB homodimer and, in combination with biochemical and in vivo data, the structure provides insight into the basis of transcriptional repression by this critical B cell lymphoma protein.

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Organizational Affiliation: 

Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A, B	127	Homo sapiens	Mutation(s): 3  Gene Names: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens) Explore P41182  Go to UniProtKB:  P41182
PHAROS:  P41182 GTEx:  ENSG00000113916

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor co-repressor 2	C, D	19	Homo sapiens	Mutation(s): 0  Gene Names: NCOR2 OR CTG26, NCOR2, CTG26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y618 (Homo sapiens) Explore Q9Y618  Go to UniProtKB:  Q9Y618
PHAROS:  Q9Y618 GTEx:  ENSG00000196498

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.228	α = 90
b = 38.543	β = 92.92
c = 76.659	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-26 
• Released Date: 2003-12-23 
Deposition Author(s): Ahmad, K.F., Melnick, A., Lax, S.A., Bouchard, D., Liu, J., Kiang, C.L., Mayer, S., Licht, J.D., Prive, G.G.

Revision History  

• Version 1.0: 2003-12-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Database references