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- PDB-4u2n: Crystal structure of a complex of the Miz1- and Nac1 POZ domains. -

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Basic information

Entry
Database: PDB / ID: 4u2n
TitleCrystal structure of a complex of the Miz1- and Nac1 POZ domains.
ComponentsZinc finger and BTB domain-containing protein 17,Nucleus accumbens-associated protein 1
KeywordsTRANSCRIPTION / POZ domain / BTB domain
Function / homology
Function and homology information


ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding ...ectoderm development / XBP1(S) activates chaperone genes / regulation of immune system process / gastrulation with mouth forming second / G1 to G0 transition / negative regulation of cell cycle / core promoter sequence-specific DNA binding / regulation of cytokine production / protein-DNA complex / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
BEN domain / BEN domain / BEN domain profile. / BEN / 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 ...BEN domain / BEN domain / BEN domain profile. / BEN / 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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 17 / Nucleus accumbens-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
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,Nucleus accumbens-associated protein 1
B: Zinc finger and BTB domain-containing protein 17,Nucleus accumbens-associated protein 1


Theoretical massNumber of molelcules
Total (without water)55,7212
Polymers55,7212
Non-polymers00
Water54030
1
A: Zinc finger and BTB domain-containing protein 17,Nucleus accumbens-associated protein 1


Theoretical massNumber of molelcules
Total (without water)27,8611
Polymers27,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12630 Å2
MethodPISA
2
B: Zinc finger and BTB domain-containing protein 17,Nucleus accumbens-associated protein 1


Theoretical massNumber of molelcules
Total (without water)27,8611
Polymers27,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.090, 115.190, 58.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a dimer. There are two biological units in the asymmetric unit.

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Components

#1: Protein Zinc finger and BTB domain-containing protein 17,Nucleus accumbens-associated protein 1 / 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 / NAC-1 / BTB/POZ domain-containing protein 14B


Mass: 27860.744 Da / Num. of mol.: 2 / Fragment: UNP residues 2-115,UNP residues 2-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB17, MIZ1, ZNF151, ZNF60, NACC1, BTBD14B, NAC1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13105, UniProt: Q96RE7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.2 % PEG 4000, 0.1 M sodium citrate pH 5.6

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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: 2.3→50.93 Å / Num. obs: 33315 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 24
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.84 Å50.93 Å
Translation6.84 Å50.93 Å

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Processing

Software
NameVersionClassification
XDS2.5.6data reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0071refinement
Aimlessdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U2M

4u2m


Resolution: 2.3→50.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2814 / WRfactor Rwork: 0.2344 / FOM work R set: 0.74 / SU R Cruickshank DPI: 0.2555 / SU Rfree: 0.2267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2863 1657 5 %RANDOM
Rwork0.2377 31610 --
obs0.2402 33267 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.07 Å2 / Biso mean: 64.693 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å2-0 Å2
2--1.57 Å20 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 2.3→50.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 0 30 3592
Biso mean---65.88 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193648
X-RAY DIFFRACTIONr_bond_other_d00.023416
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9444949
X-RAY DIFFRACTIONr_angle_other_deg3.66437809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93225.38171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40615587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.959159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024227
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02876
X-RAY DIFFRACTIONr_mcbond_it6.3456.3231862
X-RAY DIFFRACTIONr_mcbond_other6.3476.3221861
X-RAY DIFFRACTIONr_mcangle_it8.2249.4392318
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 105 -
Rwork0.347 2306 -
all-2411 -
obs--99.71 %

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