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- PDB-2q81: Crystal Structure of the Miz-1 BTB/POZ domain -

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Basic information

Entry
Database: PDB / ID: 2q81
TitleCrystal Structure of the Miz-1 BTB/POZ domain
ComponentsMiz-1 protein
KeywordsTRANSCRIPTION / BTB/POZ 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding
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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStead, M.A. / Trinh, C.H. / Garnett, J.A. / Carr, S.B. / Edwards, T.A. / Wright, S.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: A Beta-Sheet Interaction Interface Directs the Tetramerisation of the Miz-1 POZ Domain
Authors: Stead, M.A. / Trinh, C.H. / Garnett, J.A. / Carr, S.B. / Baron, A.J. / Edwards, T.A. / Wright, S.C.
History
DepositionJun 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Miz-1 protein
B: Miz-1 protein
C: Miz-1 protein
D: Miz-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4785
Polymers52,2844
Non-polymers1941
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-64 kcal/mol
Surface area19550 Å2
MethodPISA, PQS
2
A: Miz-1 protein
B: Miz-1 protein
C: Miz-1 protein
D: Miz-1 protein
hetero molecules

A: Miz-1 protein
B: Miz-1 protein
C: Miz-1 protein
D: Miz-1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,95610
Polymers104,5688
Non-polymers3882
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area20070 Å2
ΔGint-132 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.535, 128.522, 116.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer

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Components

#1: Protein
Miz-1 protein / Zinc finger and BTB domain-containing protein 17 / Zinc finger protein 151 / Myc-interacting zinc ...Zinc finger and BTB domain-containing protein 17 / Zinc finger protein 151 / Myc-interacting zinc finger protein


Mass: 13071.004 Da / Num. of mol.: 4 / Fragment: BTB domain, residues 2-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB17, MIZ1, ZNF151 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q13105
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 20% PEG 400, 200 mM MgCl2, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2006 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→64.26 Å / Num. all: 28942 / Num. obs: 28911 / % possible obs: 99.8 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.6 / Redundancy: 6.1 % / Biso Wilson estimate: 31.314 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 21.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.1 / Num. unique all: 4177 / Rsym value: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2nn2

2nn2


Resolution: 2.1→12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.685 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1456 5.1 %RANDOM
Rwork0.181 ---
obs0.184 28747 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.833 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---1.26 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 13 239 3804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223657
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.9484958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1835465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97225.976169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31515629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.156154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022716
X-RAY DIFFRACTIONr_nbd_refined0.2140.21667
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.210
X-RAY DIFFRACTIONr_mcbond_it0.6671.52373
X-RAY DIFFRACTIONr_mcangle_it1.0823691
X-RAY DIFFRACTIONr_scbond_it1.62331419
X-RAY DIFFRACTIONr_scangle_it2.4944.51262
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 116 -
Rwork0.188 1936 -
obs-2052 100 %
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)
13.1128-0.75-0.54053.0810.6821.60070.0541-0.11730.06110.3602-0.14650.2291-0.1538-0.26910.09240.0809-0.02180.02950.1065-0.0389-0.05323.90126.256247.4601
22.86850.4685-1.03963.8448-0.37781.09920.0806-0.19460.3538-0.0194-0.1032-0.661-0.20690.09210.02260.0492-0.0875-0.0365-0.0062-0.03420.14748.514331.979942.497
36.17592.4423-1.99237.6258-0.71013.49050.0365-0.4233-0.9676-0.0518-0.4837-2.02230.43180.81870.4472-0.01940.08130.02180.14330.17820.442153.89234.282841.3613
43.18470.28950.44395.0904-0.96051.5840.1556-0.179-0.5091-0.0701-0.05970.29460.396-0.0583-0.09590.1172-0.0726-0.01280.00810.05350.016229.06-1.1443.4805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1145 - 118
2X-RAY DIFFRACTION2BB2 - 1146 - 118
3X-RAY DIFFRACTION3CC1 - 1145 - 118
4X-RAY DIFFRACTION4DD2 - 1146 - 118

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