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- PDB-4u2m: Crystal structure of a complex of the Miz1- and BCL6 POZ domains. -

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Basic information

Entry
Database: PDB / ID: 4u2m
TitleCrystal structure of a complex of the Miz1- and BCL6 POZ domains.
ComponentsZinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
KeywordsTRANSCRIPTION / POZ domain / BTB domain
Function / homology
Function and homology information


ectoderm development / XBP1(S) activates chaperone genes / 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 ...ectoderm development / XBP1(S) activates chaperone genes / 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 / gastrulation with mouth forming second / 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 / G1 to G0 transition / 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 / negative regulation of cell cycle / 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 / core promoter sequence-specific DNA binding / 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 / protein-DNA complex / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription coactivator binding / cell morphogenesis / sequence-specific double-stranded DNA binding / intracellular protein localization / heterochromatin formation / regulation of cell population proliferation / actin cytoskeleton organization / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / inflammatory response / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
C2H2-type zinc finger / 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. ...C2H2-type zinc finger / 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 / Zinc finger and BTB domain-containing protein 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsStead, M.A. / Wright, S.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Yorkshire Cancer ResearchL334 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structures of heterodimeric POZ domains of Miz1/BCL6 and Miz1/NAC1.
Authors: Stead, M.A. / Wright, S.C.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
B: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
C: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein
D: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)113,3114
Polymers113,3114
Non-polymers00
Water2,936163
1
A: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein


Theoretical massNumber of molelcules
Total (without water)28,3281
Polymers28,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.850, 97.880, 119.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are four biological units in the asymmetric unit.

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Components

#1: Protein
Zinc finger and BTB domain-containing protein 17,B-cell lymphoma 6 protein / Myc-interacting zinc finger protein 1 / Miz-1 / Zinc finger protein 151 / Zinc finger protein 60 / ...Myc-interacting zinc finger protein 1 / Miz-1 / Zinc finger protein 151 / Zinc finger protein 60 / 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: 28327.648 Da / Num. of mol.: 4
Fragment: POZ domain, UNP residues 2-115,POZ domain, UNP residues 5-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ZBTB17, MIZ1, ZNF151, ZNF60, BCL6, BCL5, LAZ3, ZBTB27, ZNF51
Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13105, UniProt: P41182
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 4 % PEG 3350, 3 % 2-propanol, 0.2 M ammonium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2014
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.23→58.47 Å / Num. obs: 52962 / % possible obs: 99.3 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.025 / Net I/σ(I): 19 / Num. measured all: 215105
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.23-2.293.90.3114.81463337380.9190.17396.2
9.97-58.473.40.02150.823046690.990.01398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.77 Å58.47 Å
Translation5.77 Å58.47 Å

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
XDSdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
ARPmodel building
REFMAC5.8.0073refinement
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→58.47 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.198 / FOM work R set: 0.8008 / SU B: 6.899 / SU ML: 0.169 / SU R Cruickshank DPI: 0.2853 / SU Rfree: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 2580 4.9 %RANDOM
Rwork0.2114 50287 --
obs0.2129 52867 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.85 Å2 / Biso mean: 46.076 Å2 / Biso min: 24.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å20 Å2
2--1.61 Å20 Å2
3----2.36 Å2
Refinement stepCycle: final / Resolution: 2.23→58.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7161 0 0 163 7324
Biso mean---50.29 -
Num. residues----941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197305
X-RAY DIFFRACTIONr_bond_other_d0.0080.026993
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9529912
X-RAY DIFFRACTIONr_angle_other_deg1.457315953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29724.613310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7541529
X-RAY DIFFRACTIONr_chiral_restr0.0850.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028319
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021702
X-RAY DIFFRACTIONr_mcbond_it3.9854.4873765
X-RAY DIFFRACTIONr_mcbond_other3.9824.4863764
X-RAY DIFFRACTIONr_mcangle_it5.5346.7044689
LS refinement shellResolution: 2.23→2.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.582 160 -
Rwork0.589 3532 -
all-3692 -
obs--95.08 %

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