6ZBU

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

PDB DOI: https://doi.org/10.2210/pdb6ZBU/pdb

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

Deposited: 2020-06-09 Released: 2020-12-02
Deposition Author(s): Zacharchenko, T., Wright, S.C.
Funding Organization(s): Kay Kendall Leukaemia Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.259
R-Value Work: 0.224
R-Value Observed: 0.226

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

PubMed: 33708392 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 108.33 kDa
Atom Count: 7,421
Modelled Residue Count: 883
Deposited Residue Count: 924
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor corepressor 1,B-cell lymphoma 6 protein	A B E F H [auth I] A, B, E, F, H [auth I], I [auth J]	137	Homo sapiens	Mutation(s): 0 Gene Names: NCOR1, KIAA1047, 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
Find proteins for O75376 (Homo sapiens) Explore O75376 Go to UniProtKB: O75376
PHAROS: O75376 GTEx: ENSG00000141027
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	O75376P41182
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor corepressor 1	C D G J [auth K] K [auth L] C, D, G, J [auth K], K [auth L], L [auth H]	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75376
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain IA [auth I] SDF format, chain KA [auth J] SDF format, chain LA [auth J] SDF format, chain M [auth A] SDF format, chain MA [auth J] SDF format, chain N [auth A] SDF format, chain NA [auth J] SDF format, chain O [auth A] SDF format, chain OA [auth J] SDF format, chain P [auth A] SDF format, chain PA [auth K] SDF format, chain QA [auth L] SDF format, chain R [auth B] SDF format, chain RA [auth H] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain KA [auth J] MOL2 format, chain LA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth K] MOL2 format, chain QA [auth L] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E]	AA [auth E] BA [auth E] CA [auth F] DA [auth G] EA [auth G] AA [auth E], BA [auth E], CA [auth F], DA [auth G], EA [auth G], FA [auth G], GA [auth I], HA [auth I], IA [auth I], KA [auth J], LA [auth J], M [auth A], MA [auth J], N [auth A], NA [auth J], O [auth A], OA [auth J], P [auth A], PA [auth K], QA [auth L], R [auth B], RA [auth H], S [auth B], T [auth B], U [auth B], W [auth D], Y [auth E], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth K] Focus chain QA [auth L] Focus chain R [auth B] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth K] Focus chain QA [auth L] Focus chain R [auth B] Focus chain RA [auth H] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain JA [auth I] SDF format, chain Q [auth A] SDF format, chain V [auth C] SDF format, chain X [auth D] MOL2 format, chain JA [auth I] MOL2 format, chain Q [auth A] MOL2 format, chain V [auth C] MOL2 format, chain X [auth D]	JA [auth I], Q [auth A], V [auth C], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain JA [auth I] Focus chain Q [auth A] Focus chain V [auth C] Focus chain X [auth D] Interactions & Density Focus chain JA [auth I] Focus chain Q [auth A] Focus chain V [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.259
R-Value Work: 0.224
R-Value Observed: 0.226
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.575	α = 90
b = 198.575	β = 90
c = 113.067	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Zacharchenko, T.

Wright, S.C.

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

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

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Help and Resources

6ZBU

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2