3bim

Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor peptide

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

B-cell lymphoma 6 protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	BCL-6 corepressor × 2 （Q6W2J9） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	BCL-6 corepressor × 2 （Q6W2J9） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	BCL-6 corepressor × 2 （Q6W2J9） water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	BCL-6 corepressor × 2 （Q6W2J9） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCL6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–127； UniProt 5–129 Author chain B； PDBConstruct 3–127； UniProt 5–129 Author chain C； PDBConstruct 3–127； UniProt 5–129 Author chain D； PDBConstruct 3–127； UniProt 5–129 Author chain E； PDBConstruct 3–127； UniProt 5–129 Author chain F； PDBConstruct 3–127； UniProt 5–129 Author chain G； PDBConstruct 3–127； UniProt 5–129 Author chain H； PDBConstruct 3–127； UniProt 5–129

BCL-6 corepressor

Homo sapiens

UniProt Q6W2J9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	B-cell lymphoma 6 protein × 2 （P41182） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	B-cell lymphoma 6 protein × 2 （P41182） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	B-cell lymphoma 6 protein × 2 （P41182） water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	B-cell lymphoma 6 protein × 2 （P41182） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BCOR_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 3–19； UniProt 498–514 Author chain J； PDBConstruct 3–19； UniProt 498–514 Author chain K； PDBConstruct 3–19； UniProt 498–514 Author chain L； PDBConstruct 3–19； UniProt 498–514 Author chain M； PDBConstruct 3–19； UniProt 498–514 Author chain N； PDBConstruct 3–19； UniProt 498–514 Author chain O； PDBConstruct 3–19； UniProt 498–514 Author chain P； PDBConstruct 3–19； UniProt 498–514

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3bim
Deposition date deposition_date	2007-11-30
Structure title title	Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor peptide
Keywords keywords	;protein-peptide compex, Activator, Chromosomal rearrangement, DNA-binding, Metal-binding, Nucleus, Phosphoprotein, Polymorphism, Proto-oncogene, Repressor, Transcription, Transcription regulation, Zinc, Zinc-finger, Alternative splicing, ANK repeat, Chromatin regulator, Disease mutation, TRANSCRIPTION REPRESSOR ;; TRANSCRIPTION REPRESSOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3bim__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3bim__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bim__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.89 Å
Rg (electron density)	19.97 Å
Total Rg	20.98 Å
Atom count	2247
Residues	282
Excluded volume	40275 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bim__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bim__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bim__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3bim__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	B-cell lymphoma 6 protein
Molecular weight formula_weight	14559.8 kDa
Mutation mutation	C8Q, C67R, C84N
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	9091

GSADSQIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINLDPEINPEGFNILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	BCL-6 corepressor
Molecular weight formula_weight	1928.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O,P

GSRSEIISTAPSSWVVPGP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3bima_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d3bimb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d3bimc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d3bimd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d3bime_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d3bimf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d3bimg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

Domain ID domain_id	d3bimh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

CATH v4.4 (8 domains)

Domain ID domain_id	3bimA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	3bimB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	3bimC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	3bimD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	3bimE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	3bimF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	3bimG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

Domain ID domain_id	3bimH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

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Unit-cell length a length_a	150.550 Å
Unit-cell length b length_b	150.550 Å
Unit-cell length c length_c	312.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	96

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	48.700 Å
R factor r_factor	0.2210
R_work r_work	0.2190
R_free r_free	0.2600

Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

B-cell lymphoma 6 protein

State in the Current Structure

Other States of the Same Protein in the Database

BCL-6 corepressor

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bim__assembly_1__model_1

3bim__assembly_1__model_1 | I(q)

3bim__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the BCL6 BTB domain dimer in complex with the BCOR BBD corepressor peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

B-cell lymphoma 6 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

BCL-6 corepressor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bim__assembly_1__model_1

3bim__assembly_1__model_1 | I(q)

3bim__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)