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- PDB-5h7g: Crystal structure of the BCL6 BTB domain in complex with F1324 -

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Basic information

Entry
Database: PDB / ID: 5h7g
TitleCrystal structure of the BCL6 BTB domain in complex with F1324
Components
  • B-cell lymphoma 6 protein
  • F1324 peptide
KeywordsTranscription/Inhibitor / Transcription Repressor / Complex / Inhibitor / Transcription-Inhibitor complex
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 isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation ...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 isotype switching to IgE isotypes / negative regulation of plasma cell differentiation / negative regulation of T-helper 2 cell differentiation / isotype switching to IgE isotypes / negative regulation of mononuclear cell proliferation / negative regulation of mast cell cytokine production / regulation of germinal center formation / plasma cell differentiation / paraspeckles / germinal center formation / pyramidal neuron differentiation / type 2 immune response / regulation of immune system process / positive regulation of regulatory T cell differentiation / T-helper 2 cell differentiation / negative regulation of B cell apoptotic process / positive regulation of cell motility / negative regulation of Rho protein signal transduction / FOXO-mediated transcription of cell death genes / negative regulation of cell-matrix adhesion / regulation of T cell proliferation / negative regulation of Notch signaling pathway / B cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / regulation of cell differentiation / negative regulation of cellular senescence / Rho protein signal transduction / regulation of immune response / erythrocyte development / heterochromatin formation / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / cell morphogenesis / protein localization / 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 / actin cytoskeleton organization / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / inflammatory response / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / Golgi apparatus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / metal ion binding
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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / 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)
Enterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSogabe, S. / Ida, K. / Lane, W. / Snell, G.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Discovery of high-affinity BCL6-binding peptide and its structure-activity relationship.
Authors: Sakamoto, K. / Sogabe, S. / Kamada, Y. / Sakai, N. / Asano, K. / Yoshimatsu, M. / Ida, K. / Imaeda, Y. / Sakamoto, J.I.
History
DepositionNov 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: F1324 peptide
D: F1324 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2186
Polymers36,0264
Non-polymers1922
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-64 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.797, 37.516, 82.594
Angle α, β, γ (deg.)90.00, 112.94, 90.00
Int Tables number5
Space group name H-MC121

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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: 16287.733 Da / Num. of mol.: 2 / Fragment: UNP residues 5-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51 / Production host: Escherichia coli (E. coli) / References: UniProt: P41182
#2: Protein/peptide F1324 peptide


Mass: 1725.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M imidazole pH 6.5, 0.2M lithium sulfate, 25% PEG 3350, 15% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 23655 / % possible obs: 92.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.5
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.3 / % possible all: 54.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R28

1r28


Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.633 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28453 1143 4.9 %RANDOM
Rwork0.24357 ---
obs0.24552 22351 92.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.247 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å2-0 Å20.13 Å2
2---0.39 Å20 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 10 89 2293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192240
X-RAY DIFFRACTIONr_bond_other_d0.0020.022190
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9593028
X-RAY DIFFRACTIONr_angle_other_deg0.97434998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.50622.549102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4371522
X-RAY DIFFRACTIONr_chiral_restr0.090.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
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_it0.6611.6421076
X-RAY DIFFRACTIONr_mcbond_other0.6611.6421075
X-RAY DIFFRACTIONr_mcangle_it1.1682.4531338
X-RAY DIFFRACTIONr_mcangle_other1.1682.4531339
X-RAY DIFFRACTIONr_scbond_it0.6821.751164
X-RAY DIFFRACTIONr_scbond_other0.6821.7361160
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1212.5641684
X-RAY DIFFRACTIONr_long_range_B_refined3.33119.0642482
X-RAY DIFFRACTIONr_long_range_B_other3.29519.0442482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 52 -
Rwork0.307 1061 -
obs--60.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.58960.2032-0.2210.5726-0.14061.320.02620.001-0.0819-0.0607-0.0408-0.1038-0.02390.20010.01460.0248-0.01430.02220.176-0.0050.0297-6.630914.549318.2559
21.29530.29650.0710.73690.12541.6945-0.01560.01850.1053-0.0359-0.0060.16440.0234-0.27020.02160.0083-0.0128-0.00380.1863-0.0010.0413-26.218713.511218.5767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 128
2X-RAY DIFFRACTION1C801 - 813
3X-RAY DIFFRACTION2B7 - 128
4X-RAY DIFFRACTION2D801 - 813

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