6XYX: BCL6 BTB domain

Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD corepressor peptide. Determined by X-ray diffraction at 1.44 Å resolution. Released 2 Dec 2020.

Method: X-ray diffraction
Resolution: 1.44 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,506
Mol. weight: 32.99 kDa
Released: 2 Dec 2020

Explore 6XYX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XYX contains 15 α-helices and 12 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
α-helix	14-27	14
β-strand	34-38	5	2
β-strand	41-45	5	2
α-helix	47-53	7
α-helix	55-61	7
β-strand	71-73	3	2
α-helix	80-92	13
β-strand	94-96	3	3
α-helix	102-111	10
α-helix	115-123	9

Chain B: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	3
α-helix	14-27	14
β-strand	34-38	5	4
β-strand	41-45	5	4
α-helix	47-53	7
α-helix	55-60	6
β-strand	71-73	3	4
α-helix	74-75	2
α-helix	80-92	13
β-strand	94-97	4	1
α-helix	102-111	10
α-helix	115-122	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1342-1346	5	1
α-helix	1352-1355	4

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	1343-1346	4	3
α-helix	1352-1355	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B-cell lymphoma 6 protein	A, B	protein	126	Homo sapiens	P41182 (AlphaFold model)
Nuclear receptor corepressor 1	C, D	protein	17	Homo sapiens	O75376 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6XYX_1 B-cell lymphoma 6 protein (chains A, B)
GPDSQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTD
QLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRK
FIKASE

Sequence of entity 2 (C, D), FASTA

>6XYX_2 Nuclear receptor corepressor 1 (chains C, D)
GITTIKEMGRSIHEIPR

Primary citation

Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone. Zacharchenko, T., Wright, S. IUCrJ (2021) 8:154-160. DOI 10.1107/S2052252520015754 · PubMed

Other PDB entries of the same protein (UniProt P41182 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7LWE 1.17 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-7629
7RV1 1.17 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8826
7OKL 1.2 Å, Crystal structure of human BCL6 BTB domain in complex with compound 13e
7LWF 1.22 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-9320
7RV4 1.25 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-9153
7RV8 1.25 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-10268
7RUY 1.27 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8388
7RV2 1.29 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8828
1R29 1.3 Å, Crystal Structure of the B-Cell Lymphoma 6 (BCL6) BTB Domain to 1.3 Angstrom
7LWG 1.3 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-12694
7RUW 1.3 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-7859
7RUX 1.3 Å, Crystal structure of the BCL6 BTB domain in complex with OICR-8311

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