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

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Basic information

Entry
Database: PDB / ID: 7gvh
TitleCrystal Structure of B-cell lymphoma 6 protein BTB domain in complex with ligand 3 at 15.95 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: 1.85 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)15,5565
Polymers15,1482
Non-polymers4093
Water2,900161
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)31,11310
Polymers30,2954
Non-polymers8176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area7290 Å2
ΔGint-85 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.640, 67.640, 166.570
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-310-

HOH

21A-378-

HOH

31A-381-

HOH

41A-449-

HOH

51A-451-

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, 164 molecules

#3: Chemical ChemComp-A1ACL / 5-[(5,6-dichloropyrimidin-4-yl)amino]-1,3-dihydro-2H-indol-2-one


Mass: 295.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8Cl2N4O / Source: (synth.) synthetic construct (others) / 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.: 161 / 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: 3.63 Å3/Da / Density % sol: 66.12 %
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: 1.85→33.94 Å / Num. obs: 19870 / % possible obs: 99.4 % / Redundancy: 9.1 % / Biso Wilson estimate: 32.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.034 / Rrim(I) all: 0.103 / Net I/σ(I): 10.9 / Num. measured all: 180496 / Scaling rejects: 654
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
1.85-1.899.21.5431124012210.650.5211.6311.4100
9.06-33.947.10.0415102130.9980.0160.04332.895.7

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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: 1.85→33.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1047 5.28 %RANDOM
Rwork0.18 ---
obs0.181 19832 98.7 %-
Displacement parametersBiso max: 122.81 Å2 / Biso mean: 37.89 Å2 / Biso min: 18.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.1938 Å20 Å20 Å2
2---1.1938 Å20 Å2
3---2.3877 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.85→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 23 161 1207
Biso mean--36.77 55.29 -
Num. residues----130
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d430SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes229HARMONIC5
X-RAY DIFFRACTIONt_it1198HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion158SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance6HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1545SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1198HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1642HARMONIC20.89
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion14.95
LS refinement shellResolution: 1.85→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.241 145 5.12 %
Rwork0.2529 2686 -
all0.2523 2831 -
obs--99.3 %
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)
11.09530.248-0.36761.98871.36421.96090.0917-0.03060.11010.2618-0.03240.06840.0330.0195-0.0593-0.0146-0.02810.0164-0.0815-0.0092-0.015829.269-16.626123.9726
20.57210.1673-0.07630.00250.319100.0153-0.00130.0135-0.0119-0.00310.03190.01620.0225-0.0122-0.1267-0.0382-0.03150.0822-0.07780.013819.1087-32.34051.8784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|6 - 129}A6 - 129
2X-RAY DIFFRACTION2{D|1 - 5}D1 - 5

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