6XZZ | pdb_00006xzz

Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD2 peptide

• PDB DOI: https://doi.org/10.2210/pdb6XZZ/pdb

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


• Deposited: 2020-02-05 Released: 2020-12-02 
• Deposition Author(s): Zacharchenko, T., Wright, S.C.
• Funding Organization(s): Kay Kendall Leukaemia Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone.

Zacharchenko, T., Wright, S.

(2021) IUCrJ 8: 154-160

• PubMed: 33708392 
• DOI: https://doi.org/10.1107/S2052252520015754
• Primary Citation Related Structures: 
  6XWF, 6XXS, 6XYX, 6XZZ, 6Y17, 6ZBU


• PubMed Abstract: 
  

  The production of diffraction-quality protein crystals is challenging and often requires bespoke, time-consuming and expensive strategies. A system has been developed in which the BCL6 BTB domain acts as a crystallization chaperone and promiscuous assembly block that may form the basis for affinity-capture crystallography. The protein of interest is expressed with a C-terminal tag that interacts with the BTB domain, and co-crystallization leads to its incorporation within a BTB-domain lattice. This strategy was used to solve the structure of the SH3 domain of human nebulin, a structure previously solved by NMR, at 1.56 Å resolution. This approach is simple and effective, requiring only routine protein complexation and crystallization screening, and should be applicable to a range of proteins.

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Organizational Affiliation: 
• School of Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse, Leeds LS2 9JT, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.71 kDa 
• Atom Count: 1,257 
• Modeled Residue Count: 132 
• Deposited Residue Count: 143 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A	126	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 corepressor 1	B	17	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens) Explore O75376  Go to UniProtKB:  O75376
PHAROS:  O75376 GTEx:  ENSG00000141027

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	L [auth B]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
CL	J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.014	α = 90
b = 67.014	β = 90
c = 152.016	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Zacharchenko, T., Wright, S.C.

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Funding Organization	Location	Grant Number
Kay Kendall Leukaemia Fund	United Kingdom	KKLF1047

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references
• Version 1.2: 2021-03-24
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description