3E4U

Crystal Structure of the Wild-Type Human BCL6 BTB/POZ Domain

• PDB DOI: https://doi.org/10.2210/pdb3E4U/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-12 Released: 2008-12-09 
• Deposition Author(s): Stead, M.A., Rosbrook, G.O., Hadden, J.M., Trinh, C.H., Carr, S.B., Wright, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.259 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Structure of the wild-type human BCL6 POZ domain.

Stead, M.A., Rosbrook, G.O., Hadden, J.M., Trinh, C.H., Carr, S.B., Wright, S.C.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 1101-1104

• PubMed: 19052359 
• DOI: https://doi.org/10.1107/S1744309108036063
• Primary Citation of Related Structures:  
  3E4U


• PubMed Abstract: 
  

  BCL6 is a transcriptional repressor that is overexpressed in diffuse large B-cell lymphoma and follicular lymphoma. The N-terminal POZ domain of BCL6 interacts with transcriptional corepressors and targeting these associations is a promising therapeutic strategy. Previous structural studies of the BCL6 POZ domain have used a mutant form because of the low solubility of the wild-type recombinant protein. A method for the purification and crystallization of the wild-type BCL6 POZ domain is described and the crystal structure to 2.1 A resolution is reported. This will be relevant for the design of therapeutics that target BCL6 POZ-domain interaction interfaces.

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Organizational Affiliation: 

Molecular Cell Biology Research Group, Garstang/Astbury Buildings, Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 88.42 kDa 
• Atom Count: 5,827 
• Modelled Residue Count: 698 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A, B, C, D, E, F	130	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.259 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.209	α = 90
b = 59.209	β = 90
c = 158.971	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Stead, M.A., Rosbrook, G.O., Hadden, J.M., Trinh, C.H., Carr, S.B., Wright, S.C.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-28
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references