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- PDB-7gw0: Crystal Structure of B-cell lymphoma 6 protein BTB domain in comp... -

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Basic information

Entry
Database: PDB / ID: 7gw0
TitleCrystal Structure of B-cell lymphoma 6 protein BTB domain in complex with ligand 4 at 21.00 MGy X-ray dose
Components
  • B-cell lymphoma 6 protein
  • WVIP tetrapeptide
KeywordsTRANSCRIPTION / transcription factor / radiation damage / ligand
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 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 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 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 / 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 / regulation of cell differentiation / regulation of T cell proliferation / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / B cell proliferation / negative regulation of cellular senescence / negative regulation of Notch signaling pathway / negative regulation of cell-matrix adhesion / Rho protein signal transduction / regulation of immune response / erythrocyte development / positive regulation of B cell proliferation / regulation of cytokine production / positive regulation of neuron differentiation / cell-matrix adhesion / transcription corepressor binding / cell motility / negative regulation of cell growth / cell morphogenesis / chromatin DNA binding / heterochromatin formation / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / protein localization / regulation of cell population proliferation / regulation of inflammatory response / actin cytoskeleton organization / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / spermatogenesis / 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
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
Similarity search - Domain/homology
: / B-cell lymphoma 6 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.9 Å
AuthorsRodrigues, M.J. / Le Bihan, Y.V. / van Montfort, R.L.M.
CitationJournal: J.Appl.Crystallogr. / Year: 2024
Title: Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures.
Authors: Rodrigues, M.J. / Cabry, M. / Collie, G. / Carter, M. / McAndrew, C. / Owen, R.L. / Bellenie, B.R. / Le Bihan, Y.V. / van Montfort, R.L.M.
History
DepositionJan 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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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
D: WVIP tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5555
Polymers15,1482
Non-polymers4083
Water2,486138
1
A: B-cell lymphoma 6 protein
D: WVIP tetrapeptide
hetero molecules

A: B-cell lymphoma 6 protein
D: WVIP tetrapeptide
hetero molecules


  • defined by author&software
  • 31.1 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)31,11110
Polymers30,2954
Non-polymers8156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area7270 Å2
ΔGint-72 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.860, 67.860, 167.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-374-

HOH

31A-399-

HOH

41A-414-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AD

#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: 14536.915 Da / Num. of mol.: 1
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) / Strain (production host): BL21-AI / References: UniProt: P41182
#2: Protein/peptide WVIP tetrapeptide


Mass: 610.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 141 molecules

#3: Chemical ChemComp-A1ACR / 5-[(2,5-dichloropyridin-4-yl)amino]-1,3-dihydro-2H-indol-2-one


Mass: 294.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9Cl2N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M K2HPO4, 0.7 M NaH2PO4, 75 mM sodium acetate pH 4.5, 2% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→34.07 Å / Num. obs: 18824 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 38.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Rrim(I) all: 0.089 / Net I/σ(I): 12 / Num. measured all: 169296 / Scaling rejects: 642
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.949.41.4121098311700.7520.4831.4941.4100
9.11-34.076.30.02148523610.0080.02246.798.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
Aimless0.5.32data scaling
BUSTER2.10.3phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→34.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.123 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.212 992 5.3 %RANDOM
Rwork0.193 ---
obs0.194 18712 99.7 %-
Displacement parametersBiso max: 127.8 Å2 / Biso mean: 46.04 Å2 / Biso min: 25.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.7513 Å20 Å20 Å2
2---0.7513 Å20 Å2
3---1.5027 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.9→34.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1005 0 24 138 1167
Biso mean--38.87 61.35 -
Num. residues----128
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d398SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes213HARMONIC5
X-RAY DIFFRACTIONt_it1132HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion150SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance5HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1401SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1132HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1546HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion15.83
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2889 157 5.37 %
Rwork0.2653 2764 -
all0.2666 2921 -
obs--99.32 %
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)
11.55490.5019-0.47562.91662.02043.11550.2134-0.05630.16530.4208-0.10020.10630.0395-0.034-0.11310.0049-0.05840.0434-0.1036-0.0212-0.053829.1508-16.682524.2898
20.52-0.01520.3454-0.19080.16740.01440.0059-0.00030.0084-0.009-0.00620.01850.0140.00360.0003-0.1747-0.05-0.0240.1396-0.1360.004818.6917-32.44361.8427
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|7 - 128}A7 - 128
2X-RAY DIFFRACTION2{D|1 - 5}D1 - 5

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