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- PDB-6df5: Kaiso (ZBTB33) zinc finger DNA binding domain in complex with the... -

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Basic information

Entry
Database: PDB / ID: 6df5
TitleKaiso (ZBTB33) 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 / regulation of immune system process / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...methyl-CpG binding / regulation of immune system process / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Double Stranded RNA Binding Domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...: / Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Double Stranded RNA Binding Domain / 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
DNA / DNA (> 10) / Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.819 Å
AuthorsNikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM36643 United States
CitationJournal: Biochemistry / Year: 2020
Title: A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences.
Authors: Nikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)27,4827
Polymers27,2503
Non-polymers2324
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, NMR spectroscopy, biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-32 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.430, 184.580, 104.570
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 , 1 types, 1 molecules A

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


Mass: 16217.771 Da / Num. of mol.: 1 / Fragment: residues 471-604
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, 137 molecules

#4: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 133 / 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

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: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.819→45.492 Å / Num. obs: 38971 / % possible obs: 99.29 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.142 / Net I/σ(I): 7.07
Reflection shellResolution: 1.819→1.88 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3741 / CC1/2: 0.607 / % possible all: 96.2

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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

4f6m


Resolution: 1.819→45.492 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.46
RfactorNum. reflection% reflection
Rfree0.2406 3893 10 %
Rwork0.2106 --
obs0.2136 38928 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.819→45.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 732 4 133 1856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111898
X-RAY DIFFRACTIONf_angle_d1.122693
X-RAY DIFFRACTIONf_dihedral_angle_d25.204749
X-RAY DIFFRACTIONf_chiral_restr0.047283
X-RAY DIFFRACTIONf_plane_restr0.005215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.819-1.86130.46882470.4292218X-RAY DIFFRACTION94
1.8613-1.90790.39212540.38052289X-RAY DIFFRACTION100
1.9079-1.95940.37462570.35952309X-RAY DIFFRACTION100
1.9594-2.01710.33432590.33062339X-RAY DIFFRACTION100
2.0171-2.08220.32062540.31272284X-RAY DIFFRACTION100
2.0822-2.15660.29632580.27492313X-RAY DIFFRACTION99
2.1566-2.2430.28572590.26272339X-RAY DIFFRACTION100
2.243-2.3450.29152590.24842331X-RAY DIFFRACTION100
2.345-2.46870.25792600.23162332X-RAY DIFFRACTION99
2.4687-2.62330.26172580.21282328X-RAY DIFFRACTION99
2.6233-2.82580.25222600.2212342X-RAY DIFFRACTION100
2.8258-3.11020.26682600.2212341X-RAY DIFFRACTION100
3.1102-3.56010.22772630.18662371X-RAY DIFFRACTION99
3.5601-4.48470.18152670.15512404X-RAY DIFFRACTION100
4.4847-45.5060.17822780.1512495X-RAY DIFFRACTION99
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)
10.9961.52280.45477.17181.33093.21590.1751-0.0614-1.0078-0.19730.0621-0.29540.92460.0041-0.05650.6634-0.0510.01590.14780.0521.017449.974193.56527.2573
23.2799-0.3090.59286.3924-1.44182.97060.06940.3123-0.59720.27020.149-1.32780.38920.3429-0.15380.30810.0145-0.07260.26230.06750.917763.0652212.490731.5937
37.7638-0.38871.19240.5416-0.88551.44850.198-0.30790.0581-0.0519-0.0651-1.03920.03170.2142-0.06380.1775-0.05090.02310.2143-0.03020.459750.7495227.172929.539
45.7135-1.4478-3.77166.5588-0.63164.31120.0195-0.44910.26790.16080.05130.33960.0075-0.0354-0.05430.1393-0.0561-0.05430.2276-0.00480.412743.6356226.102534.4732
55.2215-0.2013-0.95065.126-2.71123.1503-0.25190.7427-1.0493-0.5382-0.09990.53111.0758-0.5450.38570.3421-0.08590.02490.4062-0.0750.797335.4542223.068727.8865
65.6484.66671.69375.7656-1.39324.5952-0.34760.6571-0.4584-0.89950.4095-0.69610.56990.2991-0.08430.3575-0.05390.05210.2095-0.04960.494954.097223.19722.0009
75.14020.11441.63326.3835-3.17535.2597-0.39290.4368-0.3339-0.27630.3011-1.0288-0.20440.2515-0.11590.4349-0.16130.06650.2314-0.03210.533952.5055209.364324.7809
87.4571-1.0401-0.15086.79420.0262.9842-0.3620.7741-0.4206-0.1030.25-0.77780.9003-0.18430.04010.4488-0.09720.12090.1764-0.06740.435651.8175208.286624.3046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 482 through 517 )
2X-RAY DIFFRACTION2chain 'A' and (resid 518 through 545 )
3X-RAY DIFFRACTION3chain 'A' and (resid 546 through 552 )
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 572 )
5X-RAY DIFFRACTION5chain 'A' and (resid 573 through 583 )
6X-RAY DIFFRACTION6chain 'A' and (resid 584 through 597 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 18 )
8X-RAY DIFFRACTION8chain 'E' and (resid 19 through 36 )

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