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

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Basic information

Entry
Database: PDB / ID: 5vmu
TitleKaiso (ZBTB33) zinc finger DNA binding domain in complex with a double CpG-methylated DNA resembling the specific Kaiso binding sequence (KBS)
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*(5CM)P*GP*(5CM)P*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


methyl-CpG binding / regulation of immune system process / 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 ...methyl-CpG binding / regulation of immune system process / 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 / nucleolus / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.346 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*(5CM)P*GP*(5CM)P*GP*GP*GP*AP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5397
Polymers27,3073
Non-polymers2324
Water48627
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 area7460 Å2
ΔGint-4 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.985, 185.014, 105.108
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.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*(5CM)P*GP*(5CM)P*GP*GP*GP*AP*AP*GP*CP*A)-3')


Mass: 5584.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 31 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.: 27 / 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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1 M Di-sodium 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: 2.346→42.336 Å / Num. obs: 17827 / % possible obs: 96.24 % / Redundancy: 10.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.64
Reflection shellResolution: 2.346→2.43 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 1245 / CC1/2: 0.901 / % possible all: 67.78

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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: 2.346→42.336 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.26
RfactorNum. reflection% reflection
Rfree0.2163 1782 10.02 %
Rwork0.1787 --
obs0.1825 17789 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.346→42.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 736 4 27 1787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011960
X-RAY DIFFRACTIONf_angle_d1.1742784
X-RAY DIFFRACTIONf_dihedral_angle_d25.769752
X-RAY DIFFRACTIONf_chiral_restr0.052287
X-RAY DIFFRACTIONf_plane_restr0.005227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.346-2.40940.3855840.3503749X-RAY DIFFRACTION59
2.4094-2.48030.28211320.27261182X-RAY DIFFRACTION94
2.4803-2.56030.30561360.24241219X-RAY DIFFRACTION97
2.5603-2.65180.23551410.22891264X-RAY DIFFRACTION100
2.6518-2.7580.26921410.2341263X-RAY DIFFRACTION100
2.758-2.88350.29161400.23041260X-RAY DIFFRACTION100
2.8835-3.03550.26041400.21941258X-RAY DIFFRACTION100
3.0355-3.22560.24321410.19191263X-RAY DIFFRACTION99
3.2256-3.47450.21611410.18081269X-RAY DIFFRACTION100
3.4745-3.8240.20351420.15951284X-RAY DIFFRACTION100
3.824-4.37680.19751450.14521307X-RAY DIFFRACTION100
4.3768-5.51240.16731450.15141307X-RAY DIFFRACTION100
5.5124-42.34250.20031540.16321382X-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)
15.9123-4.7585-2.29666.6750.55574.3720.17080.03841.37070.17490.0629-0.8548-1.03070.0852-0.24370.7925-0.0424-0.02890.36640.0180.8714-13.7327-10.170125.0648
29.1514-4.01950.88154.01433.56977.0806-0.29370.15450.5854-0.30790.2833-1.4153-0.30380.4269-0.04550.47640.02880.08270.39050.0730.6899-3.762-30.541920.0646
38.91273.3184.00767.56590.47195.3592-0.0161-0.00740.16790.0702-0.14260.3343-0.2688-0.40230.10940.35420.06550.04220.32270.01040.3526-24.0771-40.848621.4557
42.519-2.5439-2.60944.966.19558.549-0.1697-0.9710.47831.3420.54150.5577-0.50150.2146-0.41380.76180.0561-0.01270.42570.04230.6158-11.6224-37.871832.0994
53.0253-1.16280.77774.64945.9189.9351-0.23250.63420.0371-2.89590.4628-1.5721.6982-0.13030.09991.9044-0.04510.13290.55490.08970.4141-17.9551-28.178512.0147
68.27192.3480.57772.41381.17135.5848-0.7328-2.1358-0.26893.02470.7701-0.7859-1.56530.8118-0.17781.49020.1272-0.5151.0391-0.15450.6401-11.1257-22.528539.383
75.06880.4815-0.91770.73071.24343.97610.2053-2.24040.14242.6279-0.1244-1.0186-0.49870.2578-0.21431.6218-0.0939-0.36131.0902-0.15390.5573-10.0801-22.353340.4935
84.7397-1.55092.24550.7828-1.05756.8849-0.01851.21640.1992-1.97770.26680.1809-1.42620.1085-0.11741.4531-0.05760.030.61780.02920.4498-20.4465-25.868413.3565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 481 through 522 )
2X-RAY DIFFRACTION2chain 'A' and (resid 523 through 545 )
3X-RAY DIFFRACTION3chain 'A' and (resid 546 through 586 )
4X-RAY DIFFRACTION4chain 'A' and (resid 587 through 601 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 8 )
6X-RAY DIFFRACTION6chain 'D' and (resid 9 through 18 )
7X-RAY DIFFRACTION7chain 'E' and (resid 19 through 28 )
8X-RAY DIFFRACTION8chain 'E' and (resid 29 through 36 )

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