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- PDB-6df9: Kaiso (ZBTB33) E535Q zinc finger DNA binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6df9
TitleKaiso (ZBTB33) E535Q zinc finger DNA binding domain in complex with the specific Kaiso binding sequence (KBS)
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
  • Transcriptional regulator Kaiso
KeywordsDNA BINDING PROTEIN/DNA / DNA methylation / Zinc finger / Transcriptional regulator / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


methyl-CpG binding / Wnt signaling pathway / sequence-specific DNA binding / intracellular signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of transcription, DNA-templated / nucleolus / nucleoplasm / plasma membrane / metal ion binding ...methyl-CpG binding / Wnt signaling pathway / sequence-specific DNA binding / intracellular signal transduction / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of transcription, DNA-templated / nucleolus / nucleoplasm / plasma membrane / metal ion binding / nucleus / cytosol
SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain profile. / BTB domain profile. / Zinc finger C2H2 type domain signature. / BTB/POZ domain / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / BTB/POZ domain
Transcriptional regulator Kaiso
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.319 Å
AuthorsNikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: To Be Published
Title: A conformational switch at the zinc finger protein Kaiso directs recognitions of specific and methylated DNA
Authors: Nikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator Kaiso
D: DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4817
Polymers27,2493
Non-polymers2324
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, NMR spectroscopy, biolayer interferometry
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-31 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)44.452, 183.142, 105.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-704-

CL

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Transcriptional regulator Kaiso / Zinc finger and BTB domain-containing protein 33


Mass: 16216.785 Da / Num. of mol.: 1 / Fragment: residues 471-604 / Mutation: E535Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB33, KAISO, ZNF348 / Plasmid: PET21D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) [DNAY] / References: UniProt: Q86T24

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DNA chain , 2 types, 2 molecules DE

#2: DNA chain DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')


Mass: 5451.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3')


Mass: 5580.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 33 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Zinc
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Chloride
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.2 M Disodium Tartrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.319→43.198 Å / Num. obs: 18818 / % possible obs: 97.72 % / Redundancy: 11.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.0614 / Rrim(I) all: 0.0683 / Net I/σ(I): 23.21
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 8.4 % / Num. unique obs: 1559 / CC1/2: 0.974 / % possible all: 82.53

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6M
Resolution: 2.319→43.198 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.27
RfactorNum. reflection% reflection
Rfree0.2178 1879 10 %
Rwork0.1722 --
Obs0.1767 18785 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.319→43.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 732 4 29 1752
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.011898
f_angle_d1.0152693
f_dihedral_angle_d25.645749
f_chiral_restr0.045283
f_plane_restr0.005215
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.319-2.38170.27851140.246102379
2.3817-2.45180.29491400.239125495
2.4518-2.53090.30681420.2384127398
2.5309-2.62140.29441480.22211338100
2.6214-2.72630.26881420.23341278100
2.7263-2.85040.28941460.21161318100
2.8504-3.00060.27071470.2141132699
3.0006-3.18860.21211460.1923131599
3.1886-3.43460.27231470.1843132399
3.4346-3.78010.21611480.16371332100
3.7801-4.32670.17661480.14851331100
4.3267-5.44940.18271510.1412135699
5.4494-43.20520.19271600.15221439100
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.13534.6144-3.72155.5214-3.15726.5950.2574-0.19760.916-0.18670.08110.5055-1.04740.0658-0.39240.80810.0136-0.05750.3578-0.06530.9666-5.6329-8.884327.1007
24.7984-2.95941.56844.7477-4.20534.16780.334-0.02251.41110.47310.04992.8942-0.3996-0.071-0.50330.72120.03260.17610.57340.00261.732-22.094-24.410930.64
38.27134.22712.77687.7529-3.57227.184-0.4697-0.50980.26791.02550.93331.9035-0.6073-0.719-0.34550.54410.07410.12450.462-0.06340.9638-16.6526-29.510832.9467
43.1366-5.4886-1.75099.83432.7912.5182-0.3256-0.4094-0.18530.12480.1550.33770.0084-0.56040.16440.3026-0.0364-0.04890.4050.00230.567-6.4033-42.172930.072
56.2147-4.57052.98533.7493-1.94467.893-0.03440.1630.1686-0.0183-0.1751-0.348-0.24630.30890.22090.3807-0.07780.0280.365-0.04320.49683.8351-39.961531.4865
66.00611.5149-3.78613.1834-5.24719.8291-0.35671.23450.7746-1.49890.90710.2132-1.6142-0.9952-0.47890.9493-0.1036-0.16270.6530.04020.7548-12.4896-37.514621.6388
77.27170.00320.56158.3214.50194.9956-0.22990.51050.1992-0.39030.13331.16830.3267-0.5747-0.24080.5934-0.1634-0.09480.38330.02860.5946-8.1171-24.685525.0643
810.1147-0.2201-1.25958.79490.29421.6486-0.31860.86040.3171-0.46830.22550.9851-0.87670.16180.02220.6457-0.0674-0.13210.30730.06650.475-7.3385-23.693624.5345
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection details
11chain 'A' and (resid 482 through 517 )
22chain 'A' and (resid 518 through 527 )
33chain 'A' and (resid 528 through 545 )
44chain 'A' and (resid 546 through 552 )
55chain 'A' and (resid 553 through 586 )
66chain 'A' and (resid 587 through 597 )
77chain 'D' and (resid 1 through 18 )
88chain 'E' and (resid 19 through 36 )

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