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- PDB-6df8: Kaiso (ZBTB33) zinc finger DNA binding domain in complex with the... -

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Basic information

Entry
Database: PDB / ID: 6df8
TitleKaiso (ZBTB33) zinc finger DNA binding domain in complex with the specific Kaiso binding sequence (KBS), pH 6.5
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


regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 ...regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
BTB/POZ domain / BTB domain profile. / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.536 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
Water1629
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 area4710 Å2
ΔGint-31 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.371, 184.267, 104.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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, 13 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.94 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Disodium tartrate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03316 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.536→43.138 Å / Num. obs: 14573 / % possible obs: 98.65 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.127 / Net I/σ(I): 10.94
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 5.3 % / Num. unique obs: 1268 / CC1/2: 0.694 / % possible all: 87.27

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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: 2.536→43.138 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.32
RfactorNum. reflection% reflection
Rfree0.2216 1452 9.98 %
Rwork0.1794 --
obs0.1838 14547 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.536→43.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 732 4 9 1749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111882
X-RAY DIFFRACTIONf_angle_d1.2142672
X-RAY DIFFRACTIONf_dihedral_angle_d26.234740
X-RAY DIFFRACTIONf_chiral_restr0.051281
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5357-2.62630.34621260.32691141X-RAY DIFFRACTION87
2.6263-2.73150.35931400.31721276X-RAY DIFFRACTION100
2.7315-2.85580.40461460.30021313X-RAY DIFFRACTION100
2.8558-3.00630.32261440.2661307X-RAY DIFFRACTION100
3.0063-3.19460.24641470.21561317X-RAY DIFFRACTION100
3.1946-3.44110.2491480.19691326X-RAY DIFFRACTION100
3.4411-3.78730.22581460.17661316X-RAY DIFFRACTION100
3.7873-4.33480.1961470.14681326X-RAY DIFFRACTION100
4.3348-5.45970.19141490.14441349X-RAY DIFFRACTION100
5.4597-43.14420.17361590.14751424X-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)
16.48724.7189-1.87985.0136-4.82828.0847-1.55570.4071-1.21150.75590.27-0.32430.70730.51491.26951.5304-0.09240.04380.46230.11581.42483.3862187.4518129.8553
27.41637.35571.29749.02784.77388.1839-0.6059-0.1914-1.0993-0.3715-0.0123-0.9072-0.1522-0.78540.55371.32270.04680.05920.49670.05151.235-1.4372191.15129.2935
37.85573.5883.93147.23394.34124.30350.063-0.2497-1.7799-0.06840.3722-0.67680.71760.1698-0.43920.90740.02120.08130.47530.06141.2719.2251196.1611133.7612
47.0607-4.0323-2.85354.8803-0.96753.77230.35750.7919-2.4871.97190.95050.61291.7489-0.6027-1.38240.95630.0351-0.12590.681-0.05362.0320.8748202.406133.945
55.61585.27092.14565.53274.19158.911-0.1611-0.5371-1.3190.4782-0.2742-3.8896-0.46830.54040.4150.89720.0185-0.13570.69920.22921.873921.4549212.6474138.2553
65.6274.7566-3.05454.0214-2.67385.7549-0.8335-0.3089-0.12230.2360.7817-0.66360.56710.26250.05540.75970.0238-0.04950.49210.06751.174615.3327216.2732136.4716
73.4496-5.27933.60758.0714-5.45194.454-1.0730.6546-0.69560.66290.02580.2366-0.26690.80321.05260.4957-0.16170.050.59570.02870.87716.4056226.6985134.4523
88.103-6.3174-3.41726.3793-0.1148.37360.07390.1192-0.3184-0.2240.02010.6390.3835-0.4775-0.06020.5212-0.1081-0.02810.3590.03350.7866-3.2607224.9835136.776
97.7335-4.40541.20553.91912.54997.87970.35150.8578-0.276-1.3442-0.0078-0.2071.7719-0.4399-0.3151.1771-0.21070.11320.6586-0.09091.05311.2437221.6215125.3211
105.5622-0.02530.37367.2161-3.10887.933-0.20490.4605-0.2337-0.27740.1994-0.92450.25470.6603-0.01080.7791-0.12150.0860.44970.00410.92228.0806209.0547129.6735
118.6423-1.3126-0.80547.35540.52076.0528-0.25730.8242-0.5523-0.19240.2338-0.7491.1812-0.11050.04940.8608-0.08530.07640.3241-0.08230.88057.3218208.0184129.244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 482 through 488 )
2X-RAY DIFFRACTION2chain 'A' and (resid 489 through 496 )
3X-RAY DIFFRACTION3chain 'A' and (resid 497 through 517 )
4X-RAY DIFFRACTION4chain 'A' and (resid 518 through 522 )
5X-RAY DIFFRACTION5chain 'A' and (resid 523 through 533 )
6X-RAY DIFFRACTION6chain 'A' and (resid 534 through 545 )
7X-RAY DIFFRACTION7chain 'A' and (resid 546 through 552 )
8X-RAY DIFFRACTION8chain 'A' and (resid 553 through 586 )
9X-RAY DIFFRACTION9chain 'A' and (resid 587 through 599)
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 18 )
11X-RAY DIFFRACTION11chain 'E' and (resid 19 through 36 )

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