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- PDB-4cp3: The structure of BCL6 BTB (POZ) domain in complex with the ansamy... -

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Basic information

Entry
Database: PDB / ID: 4cp3
TitleThe structure of BCL6 BTB (POZ) domain in complex with the ansamycin antibiotic rifabutin.
ComponentsB-CELL LYMPHOMA 6 PROTEIN
KeywordsIMMUNE SYSTEM / BTB/POZ / TRANSCRIPTIONAL REPRESSOR / RIFAMYCIN / ANTIBIOTIC / SMRT / INHIBITOR
Function / homology
Function and homology information


negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / regulation of germinal center formation / paraspeckles / negative regulation of B cell apoptotic process / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / FOXO-mediated transcription of cell death genes / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain ...negative regulation of mitotic cell cycle DNA replication / intronic transcription regulatory region sequence-specific DNA binding / regulation of germinal center formation / paraspeckles / negative regulation of B cell apoptotic process / regulation of immune system process / type 2 immune response / positive regulation of regulatory T cell differentiation / FOXO-mediated transcription of cell death genes / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of cell differentiation / regulation of immune response / regulation of cytokine production / transcription corepressor binding / negative regulation of cell growth / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / DNA damage response / negative regulation of transcription by RNA polymerase II / DNA-templated transcription / nucleoplasm / zinc ion binding / 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
RIFABUTIN / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEvans, S.E. / Fairall, L. / Goult, B.T. / Jamieson, A.G. / Ferrigno, P.K. / Ford, R. / Wagner, S.D. / Schwabe, J.W.R.
CitationJournal: Plos One / Year: 2014
Title: The Ansamycin Antibiotic, Rifamycin Sv, Inhibits Bcl6 Transcriptional Repression and Forms a Complex with the Bcl6-Btb/Poz Domain.
Authors: Evans, S.E. / Goult, B.T. / Fairall, L. / Jamieson, A.G. / Ko Ferrigno, P. / Ford, R. / Schwabe, J.W.R. / Wagner, S.D.
History
DepositionJan 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-CELL LYMPHOMA 6 PROTEIN
B: B-CELL LYMPHOMA 6 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3043
Polymers28,4572
Non-polymers8471
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-31.7 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.172, 54.828, 58.159
Angle α, β, γ (deg.)90.00, 95.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein B-CELL LYMPHOMA 6 PROTEIN / BCL-6 / B-CELL LYMPHOMA 5 PROTEIN / BCL-5 / PROTEIN LAZ-3 / ZINC FINGER AND BTB DOMAIN-CONTAINING ...BCL-6 / B-CELL LYMPHOMA 5 PROTEIN / BCL-5 / PROTEIN LAZ-3 / ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27 / ZINC FINGER PROTEIN 51


Mass: 14228.543 Da / Num. of mol.: 2 / Fragment: BTB DOMAIN, RESIDUES 9-128 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P41182
#2: Chemical ChemComp-RBT / RIFABUTIN / (9S,12E,14S,15R,16S,17R,18R,19R,20S,21S,22E,24Z)-6-16,18,20- TETRAHYDROXY-1'-ISOBUTYL-14-METHOXY-7,9,15,17,19,21,25- HEPTAMETHYLSPIRO(9,4-(EPOXYPENTADECA(1,11,13)TRIENIMINO)-2H- FURO(2',3':7,8)NAPHTH(1,2-D)IMIDAZOLE-2,4'-PIPERIDINE)- 5,10,26(3H,9H)-TRIONE,16-ACETATE / ANSAMYCIN


Mass: 847.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H62N4O11 / Comment: antibiotic, antiretroviral*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.99 Å3/Da / Density % sol: 38.17 % / Description: NONE
Crystal growpH: 5 / Details: 20% PEG 6000, 100MM SODIUM CITRATE, PH 5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.3→39.82 Å / Num. obs: 9168 / % possible obs: 97 % / Observed criterion σ(I): 4.1 / Redundancy: 3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 4.1 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R2B

1r2b


Resolution: 2.3→57.92 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.878 / SU B: 9.861 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.688 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26875 466 4.8 %RANDOM
Rwork0.19877 ---
obs0.20193 9168 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.366 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å2-0.01 Å2
2---0.11 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.3→57.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 61 23 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192063
X-RAY DIFFRACTIONr_bond_other_d0.0010.022046
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.9952794
X-RAY DIFFRACTIONr_angle_other_deg0.86334659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03423.12596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08915375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5751520
X-RAY DIFFRACTIONr_chiral_restr0.1710.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022279
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02499
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8482.609974
X-RAY DIFFRACTIONr_mcbond_other1.842.607973
X-RAY DIFFRACTIONr_mcangle_it3.0323.91214
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5943.1931089
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 45 -
Rwork0.229 664 -
obs--96.86 %

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