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- PDB-4f6n: Crystal structure of Kaiso zinc finger DNA binding protein in com... -

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Basic information

Entry
Database: PDB / ID: 4f6n
TitleCrystal structure of Kaiso zinc finger DNA binding protein in complex with methylated CpG site DNA
Components
  • DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM)P*GP*GP*TP*GP*AP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM)P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3')
  • Transcriptional regulator Kaiso
KeywordsDNA BINDING PROTEIN/DNA / zinc finger / protein-DNA complex / double helix / DNA binding / DNA / 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
Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / Double Stranded RNA Binding Domain / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily ...Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / Double Stranded RNA Binding Domain / 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
DNA / DNA (> 10) / Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBuck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.
Authors: Buck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
History
DepositionMay 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM)P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM)P*GP*GP*TP*GP*AP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1758
Polymers27,7943
Non-polymers3805
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint5 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.049, 183.402, 230.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

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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: 16086.575 Da / Num. of mol.: 1 / Fragment: zinc finger DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB33, KAISO, ZNF348 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / 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(*GP*TP*GP*TP*CP*AP*CP*(5CM)P*GP*(5CM)P*GP*TP*CP*TP*AP*TP*AP*CP*G)-3')


Mass: 5824.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs in humans / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*TP*AP*GP*AP*(5CM)P*GP*(5CM)P*GP*GP*TP*GP*AP*CP*AP*C)-3')


Mass: 5882.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs in humans / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 20 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 4.18 Å3/Da / Density % sol: 70.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M NaCl, 0.1M sodium cacodylate, 10% glycerol, 30% Peg 600, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→65 Å / Num. all: 11780 / Num. obs: 11780 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.36 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 23
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.3 / Num. unique all: 536 / Rsym value: 0.581 / % possible all: 92.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Kaiso from complex with Kaiso binding site protein

Resolution: 2.8→65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.902 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26148 558 4.7 %RANDOM
Rwork0.22847 ---
obs0.23009 11779 99.32 %-
all-11779 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.8→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 761 15 15 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211965
X-RAY DIFFRACTIONr_angle_refined_deg1.5792.4352755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3645119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.5921.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15515185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2641511
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021201
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 44 -
Rwork0.389 763 -
obs-763 94.83 %
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)
12.1190.34150.65688.74940.64781.8565-0.0354-0.0430.30290.53720.1238-0.2909-0.43510.0419-0.08850.18050.05060.03020.18840.0050.2151-14.6827-27.273724.1289
24.28320.4622-1.40295.15030.12687.52880.1324-0.82710.28440.86520.0594-0.1733-1.03750.3513-0.19180.44640.03210.06650.3147-0.01830.2965-16.8148-23.055829.4536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A481 - 600
2X-RAY DIFFRACTION2D1 - 19
3X-RAY DIFFRACTION2E21 - 38

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