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- PDB-5vmx: Kaiso (ZBTB33) zinc finger DNA binding domain in complex with a h... -

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Basic information

Entry
Database: PDB / ID: 5vmx
TitleKaiso (ZBTB33) zinc finger DNA binding domain in complex with a hemi CpG-methylated DNA resembling the specific Kaiso binding sequence (KBS)
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*CP*GP*CP*GP*GP*GP*AP*AP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*(5CM)P*GP*(5CM)P*GP*AP*AP*TP*AP*AP*CP*G)-3')
  • Transcriptional regulator Kaiso
KeywordsTRANSCRIPTION/DNA / DNA methylation / Zinc finger / Transcriptional regulator / TRANSCRIPTION-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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNikolova, E.N. / Stanfield, R.L. / Martinez-Yamout, M.A. / 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: 2018
Title: CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.
Authors: Nikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_entity_src_syn / struct_conn / struct_conn_type
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 / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3Oct 4, 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*(5CM)P*GP*(5CM)P*GP*AP*AP*TP*AP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*CP*GP*CP*GP*GP*GP*AP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5117
Polymers27,2793
Non-polymers2324
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, complex formation also monitored by NMR and biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-18 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.338, 183.984, 105.072
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*(5CM)P*GP*(5CM)P*GP*AP*AP*TP*AP*AP*CP*G)-3')


Mass: 5504.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*CP*GP*CP*GP*GP*GP*AP*AP*GP*CP*A)-3')


Mass: 5556.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 105 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: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 3.93 Å3/Da / Density % sol: 68.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1 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: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→43.104 Å / Num. obs: 27026 / % possible obs: 98.03 % / Redundancy: 10.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0891 / Net I/σ(I): 12.28
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.87 / Num. unique obs: 2370 / CC1/2: 0.941 / % possible all: 87.75

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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: 4F6N

4f6n


Resolution: 2.05→43.104 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 2700 10 %
Rwork0.1624 --
obs0.1649 27000 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→43.104 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 734 4 101 1873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011959
X-RAY DIFFRACTIONf_angle_d1.2172780
X-RAY DIFFRACTIONf_dihedral_angle_d25.012764
X-RAY DIFFRACTIONf_chiral_restr0.054289
X-RAY DIFFRACTIONf_plane_restr0.007227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.09770.22581530.22331384X-RAY DIFFRACTION85
2.0977-2.15020.22021710.19751550X-RAY DIFFRACTION95
2.1502-2.20830.24861770.19861575X-RAY DIFFRACTION97
2.2083-2.27330.23571740.18681575X-RAY DIFFRACTION98
2.2733-2.34660.20851820.18081637X-RAY DIFFRACTION99
2.3466-2.43050.21941780.17451600X-RAY DIFFRACTION99
2.4305-2.52780.18751800.18321620X-RAY DIFFRACTION99
2.5278-2.64280.1971820.16511638X-RAY DIFFRACTION100
2.6428-2.78220.22541830.18631649X-RAY DIFFRACTION100
2.7822-2.95640.21951830.18221637X-RAY DIFFRACTION100
2.9564-3.18460.20291830.18211658X-RAY DIFFRACTION100
3.1846-3.5050.17181820.16331640X-RAY DIFFRACTION100
3.505-4.01180.17571860.14361675X-RAY DIFFRACTION100
4.0118-5.05330.16011860.13471674X-RAY DIFFRACTION99
5.0533-43.11350.17552000.15361788X-RAY DIFFRACTION100
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)
14.4918-4.39174.77674.5958-4.88717.3073-0.30750.234-0.87880.30680.3807-0.32070.23850.1465-0.11980.9210.0867-0.01240.3216-0.07170.796364.8369373.042727.6828
27.5222-3.61641.65744.87270.91284.48780.11890.1663-1.1516-0.0280.09290.84550.9581-0.0405-0.23020.575-0.00240.04030.23670.00410.601257.4667379.749323.4931
37.4005-2.4260.38636.9527-1.76884.2051-0.0764-0.1643-0.7707-0.74040.22361.67240.5417-0.3336-0.19120.3424-0.0193-0.0830.3481-0.04430.603947.7163395.786920.5675
47.88581.9353-3.39176.50090.67643.77110.0497-0.0887-0.04340.13070.0239-0.29360.18940.4316-0.09420.17020.0491-0.03760.286-0.00650.215268.5978408.605221.4174
56.2128-2.79982.40325.8724-4.90314.15230.0803-0.7072-0.19051.13480.11080.22380.32420.1551-0.20370.54540.05790.03080.4327-0.01650.401556.3753405.981932.3668
64.5442-0.30030.72026.34413.63576.1614-0.1329-0.3997-0.32140.27350.18340.7420.0061-0.5038-0.21610.4140.09160.08810.34940.03540.292458.4658392.772927.6877
70.29770.6483-0.88682.5419-2.73833.71970.9297-2.4333-0.47492.2374-0.64161.07311.2431-1.19710.21371.674-0.26470.71091.35930.1670.502353.1537388.133143.6816
84.9269-0.6343-0.62614.651-0.28777.3564-0.08440.8577-0.0534-0.97940.1488-0.14650.88220.1816-0.04050.56990.02690.06160.37570.00570.260863.8298394.476316.3534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 481 through 496 )
2X-RAY DIFFRACTION2chain 'A' and (resid 497 through 517 )
3X-RAY DIFFRACTION3chain 'A' and (resid 518 through 545 )
4X-RAY DIFFRACTION4chain 'A' and (resid 546 through 586 )
5X-RAY DIFFRACTION5chain 'A' and (resid 587 through 602)
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 18 )
7X-RAY DIFFRACTION7chain 'E' and (resid 19 through 26 )
8X-RAY DIFFRACTION8chain 'E' and (resid 27 through 36 )

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