6XXS

Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with the NcoR1 BBD1 corepressor peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

Zacharchenko, T.Wright, S.

(2021) IUCrJ 8: 154-160

  • DOI: https://doi.org/10.1107/S2052252520015754
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 proteinA,
B,
G [auth F]
135Homo sapiensMutation(s): 3 
Gene Names: BCL6BCL5LAZ3ZBTB27ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
PHAROS:  P41182
GTEx:  ENSG00000113916 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41182
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor corepressor 1C,
D,
F [auth G],
H
17Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75376 (Homo sapiens)
Explore O75376 
Go to UniProtKB:  O75376
PHAROS:  O75376
GTEx:  ENSG00000141027 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75376
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
B-cell lymphoma 6 protein126Homo sapiensMutation(s): 3 
Gene Names: BCL6BCL5LAZ3ZBTB27ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens)
Explore P41182 
Go to UniProtKB:  P41182
PHAROS:  P41182
GTEx:  ENSG00000113916 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41182
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.38α = 90
b = 165.38β = 90
c = 244.8γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Kay Kendall Leukaemia FundUnited KingdomKKLF1047

Revision History  (Full details and data files)

  • 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