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- PDB-1r29: Crystal Structure of the B-Cell Lymphoma 6 (BCL6) BTB Domain to 1... -

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Basic information

Entry
Database: PDB / ID: 1r29
TitleCrystal Structure of the B-Cell Lymphoma 6 (BCL6) BTB Domain to 1.3 Angstrom
ComponentsB-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / BTB domain / B-cell lymphoma / transcriptional repression
Function / homology
Function and homology information


regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation ...regulation of memory T cell differentiation / negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / negative regulation of isotype switching to IgE isotypes / isotype switching to IgE isotypes / negative regulation of mast cell cytokine production / regulation of germinal center formation / negative regulation of mononuclear cell proliferation / plasma cell differentiation / paraspeckles / germinal center formation / regulation of immune system process / pyramidal neuron differentiation / type 2 immune response / T-helper 2 cell differentiation / positive regulation of regulatory T cell differentiation / positive regulation of cell motility / negative regulation of B cell apoptotic process / negative regulation of Rho protein signal transduction / erythrocyte development / FOXO-mediated transcription of cell death genes / regulation of cell differentiation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of T cell proliferation / B cell proliferation / negative regulation of cellular senescence / negative regulation of cell-matrix adhesion / negative regulation of Notch signaling pathway / regulation of immune response / Rho protein signal transduction / positive regulation of B cell proliferation / positive regulation of neuron differentiation / regulation of cytokine production / cell-matrix adhesion / transcription corepressor binding / cell motility / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell morphogenesis / sequence-specific double-stranded DNA binding / intracellular protein localization / heterochromatin formation / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsAhmad, K.F. / Melnick, A. / Lax, S.A. / Bouchard, D. / Liu, J. / Kiang, C.L. / Mayer, S. / Licht, J.D. / Prive, G.G.
CitationJournal: Mol.Cell / Year: 2003
Title: Mechanism of SMRT corepressor recruitment by the BCL6 BTB domain.
Authors: Ahmad, K.F. / Melnick, A. / Lax, S. / Bouchard, D. / Liu, J. / Kiang, C.L. / Mayer, S. / Takahashi, S. / Licht, J.D. / Prive, G.G.
History
DepositionSep 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Refinement description / Category: database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)14,5601
Polymers14,5601
Non-polymers00
Water3,387188
1
A: B-cell lymphoma 6 protein

A: B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)29,1202
Polymers29,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area3640 Å2
ΔGint-25 kcal/mol
Surface area12870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)30.606, 71.849, 55.414
Angle α, β, γ (deg.)90.00, 105.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1169-

HOH

21A-1170-

HOH

31A-1171-

HOH

41A-1183-

HOH

51A-1185-

HOH

DetailsThe biological assembly is a dimer, generated from the monomer in the asymmetric unit by the operations: (-X,Y,-Z) dx=-1 dy= 0 dz= 0 distance= 2.183

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Components

#1: Protein B-cell lymphoma 6 protein / BCL-6 / Zinc finger protein 51 / LAZ-3 protein / POZ domain / BTB/POZ domain


Mass: 14559.823 Da / Num. of mol.: 1 / Fragment: BTB Domain (Residues 5-129)
Mutation: Glycine and serine at N-terminus (cloning artifact), C8Q/C67R/C84N (for solubility)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6 / Plasmid: pET-32(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41182
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: sodium formate, sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
20.18 Msodium formate1reservoir
30.1 Msodium acetate1reservoirpH4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.97947, 0.97925, 0.95742, 0.8980
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979471
20.979251
30.957421
40.8981
ReflectionResolution: 1.3→30 Å / Num. all: 28377 / Num. obs: 27157 / % possible obs: 95.7 % / Redundancy: 3.7 % / Rsym value: 0.051 / Net I/σ(I): 24.4
Reflection shellResolution: 1.3→1.35 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.302 / % possible all: 93.7
Reflection
*PLUS
Highest resolution: 1.3 Å / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 93.7 % / Rmerge(I) obs: 0.302

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
SHELXL-97refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.173 1950 random
Rwork0.128 --
all0.131 26377 -
obs0.128 26377 -
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 0 188 1173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d1.53
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.1283
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_bond_d / Dev ideal: 0.013
LS refinement shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.35 Å

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