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- PDB-6v8u: Kaiso (ZBTB33) zinc finger DNA binding domain in complex with a m... -

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Basic information

Entry
Database: PDB / ID: 6v8u
TitleKaiso (ZBTB33) zinc finger DNA binding domain in complex with a modified Kaiso binding sequence (KBS)
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*CP*GP*AP*AP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*TP*TP*CP*GP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
  • Transcriptional regulator Kaiso
KeywordsDNA BINDING PROTEIN / DNA methylation / Zinc finger / Transcriptional regulator
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 / nucleus / metal ion binding / 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: 2.103 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
DepositionDec 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: 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 1.2Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.grant_number / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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
Revision 1.4Oct 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*GP*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*CP*GP*AP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5058
Polymers27,2503
Non-polymers2555
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, complex formation was was determined by NMR spectroscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-37 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.142, 183.624, 97.755
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11D-101-

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: 16217.771 Da / Num. of mol.: 1
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) / Variant (production host): [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*GP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')


Mass: 5491.566 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*CP*GP*AP*AP*GP*CP*A)-3')


Mass: 5540.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 112 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.02 M Calcium Chloride, 0.1 M Sodium Acetate, 30 % 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.103→42.92 Å / Num. obs: 23073 / % possible obs: 97.56 % / Redundancy: 11.1 % / Biso Wilson estimate: 38.8250910295 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1071 / Rrim(I) all: 0.1123 / Net I/σ(I): 17.6
Reflection shellResolution: 2.103→2.178 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.7772 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 1986 / CC1/2: 0.86 / CC star: 0.961 / % possible all: 86.23

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6M

4f6m


Resolution: 2.103→42.919 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 2307 10.01 %
Rwork0.1722 20750 -
obs0.1753 23057 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.62 Å2 / Biso mean: 56.4997 Å2 / Biso min: 22.26 Å2
Refinement stepCycle: final / Resolution: 2.103→42.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 732 5 107 1864
Biso mean--41.84 50.14 -
Num. residues----156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1033-2.1490.23711210.2649109585
2.149-2.1990.26661340.2479119790
2.199-2.2540.29391400.2446125998
2.254-2.31490.28811470.2345131899
2.3149-2.38310.29911420.2143128299
2.3831-2.460.2521450.1967130799
2.46-2.54790.27351460.1922130399
2.5479-2.64990.23941430.1918129199
2.6499-2.77050.24431460.199132198
2.7705-2.91650.25741450.2094129699
2.9165-3.09920.25781460.19231321100
3.0992-3.33840.18711470.16291331100
3.3384-3.67420.20631490.1515133799
3.6742-4.20540.13061450.1346130198
4.2054-5.29690.1711520.1393136799
5.2969-42.9190.18721590.1725142498
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)
18.84444.9822-5.8933.0434-3.00618.46120.25460.03071.155-0.19640.19580.6209-0.6684-0.0165-0.41380.569-0.0222-0.07070.2495-0.00790.6052-5.8918-8.650623.1089
26.15071.79280.19587.1133-1.61185.1981-0.23850.11890.620.3270.32412.0258-0.3438-0.3342-0.06710.3248-0.03880.01050.3437-0.03790.8107-18.7983-27.709628.4748
36.1143-1.81512.16327.4342-0.01345.2076-0.10250.478-0.0153-0.62010.137-0.0241-0.4240.2803-0.01030.2788-0.10910.01880.25720.01430.2643-1.1852-39.728825.1714
46.48290.85750.98463.34950.32074.6019-0.1076-0.62660.18590.52830.480.05640.766-0.3246-0.13920.5397-0.0076-0.0580.28-0.06410.2192-3.458-26.213332.9722
57.4362-1.08544.2991.5136-2.12194.25240.04430.8333-0.4945-1.1808-0.00520.6657-0.4962-0.6612-0.27521.0956-0.0273-0.47670.8155-0.080.4331-15.246-23.81967.9108
63.1588-2.11480.06911.6124-0.71082.48-0.47921.10720.2643-0.80.15160.6069-0.8933-0.32640.06730.9666-0.168-0.49620.64270.14350.4913-13.1201-23.528.6003
73.9081.0680.72687.6032-0.4191.76410.0136-0.85560.17310.9680.4025-0.0842-0.68650.0895-0.35740.4855-0.0346-0.08150.45450.03590.2405-1.7608-25.530235.8114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 481 through 517 )A481 - 517
2X-RAY DIFFRACTION2chain 'A' and (resid 518 through 545 )A518 - 545
3X-RAY DIFFRACTION3chain 'A' and (resid 546 through 600 )A546 - 600
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 10 )D1 - 10
5X-RAY DIFFRACTION5chain 'D' and (resid 11 through 18 )D11 - 18
6X-RAY DIFFRACTION6chain 'E' and (resid 19 through 28 )E19 - 28
7X-RAY DIFFRACTION7chain 'E' and (resid 29 through 36 )E29 - 36

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