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- PDB-5vmv: Kaiso (ZBTB33) zinc finger DNA binding domain in complex with its... -

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Basic information

Entry
Database: PDB / ID: 5vmv
TitleKaiso (ZBTB33) zinc finger DNA binding domain in complex with its double CpG-methylated DNA consensus binding site
Components
  • DNA (5'-D(*TP*GP*CP*TP*TP*CP*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / 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 / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / 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 / zinc ion binding / nucleoplasm / nucleus / 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 / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / 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: 2.313 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 / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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 / _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*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')
E: DNA (5'-D(*TP*GP*CP*TP*TP*CP*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5397
Polymers27,3073
Non-polymers2324
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, complex formation also monitored by NMR and biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-15 kcal/mol
Surface area11470 Å2
Unit cell
Length a, b, c (Å)44.219, 183.792, 104.566
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

21A-846-

HOH

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Components

#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
#2: DNA chain DNA (5'-D(*TP*GP*CP*TP*TP*CP*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')


Mass: 5544.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.89 Å3/Da / Density % sol: 68.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M Ammonium Acetate, 30 % (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.313→45.443 Å / Num. obs: 17383 / % possible obs: 90.81 % / Redundancy: 6 % / Biso Wilson estimate: 35.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08636 / Net I/σ(I): 13.11
Reflection shellResolution: 2.313→2.396 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.2765 / Mean I/σ(I) obs: 4.29 / Num. unique obs: 946 / CC1/2: 0.945 / % possible all: 51.16

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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: 2.313→45.443 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1738 10.01 %
Rwork0.203 --
obs0.2075 17361 90.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.313→45.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 736 4 76 1799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112116
X-RAY DIFFRACTIONf_angle_d1.2033012
X-RAY DIFFRACTIONf_dihedral_angle_d27.666822
X-RAY DIFFRACTIONf_chiral_restr0.05315
X-RAY DIFFRACTIONf_plane_restr0.005221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3135-2.38160.2967770.2229692X-RAY DIFFRACTION50
2.3816-2.45840.2331970.2323863X-RAY DIFFRACTION61
2.4584-2.54630.3081310.23441175X-RAY DIFFRACTION84
2.5463-2.64820.26281490.23531341X-RAY DIFFRACTION95
2.6482-2.76870.26881570.2321412X-RAY DIFFRACTION98
2.7687-2.91470.26851570.21331409X-RAY DIFFRACTION100
2.9147-3.09720.25651560.22071410X-RAY DIFFRACTION100
3.0972-3.33630.28231590.21981437X-RAY DIFFRACTION100
3.3363-3.67190.24861610.18891439X-RAY DIFFRACTION100
3.6719-4.20290.22361590.17361432X-RAY DIFFRACTION100
4.2029-5.2940.21151630.17541471X-RAY DIFFRACTION100
5.294-45.45180.24941720.21831542X-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)
10.7296-1.792-0.66775.49210.40511.9339-0.1111-0.2972-0.6070.34740.0726-0.09770.43790.1881-0.30060.88130.0558-0.02040.1874-0.12951.289820.6944.886527.6925
23.85942.68362.43784.04731.8574.79640.08720.2245-0.4898-0.11870.20120.2610.50840.2725-0.20640.72430.04430.00360.0781-0.16341.053217.03179.4921.9111
30.5135-0.53240.64682.53730.14481.36880.1431-0.2746-0.7745-0.0790.28941.42170.863-0.29820.09510.4353-0.1216-0.03460.19090.02321.44475.525818.742223.5479
41.08531.23840.46691.57580.12421.28080.18210.0191-0.332-0.5424-0.00750.89310.3983-0.2259-0.25820.53650.0207-0.28110.0277-0.14321.31262.125424.762818.0569
51.5341-1.19440.49772.214-2.29134.7098-0.1007-0.1025-0.4803-0.03480.37760.32130.0726-0.3137-0.28030.38770.028-0.0380.2296-0.08150.65986.82331.649621.0907
67.65570.8547-2.0680.71970.6411.76310.00770.3741-0.0117-0.1465-0.02740.37590.070.0418-0.02930.20660.0481-0.05070.15610.00460.401621.243841.528919.3166
76.2006-3.1204-5.53455.08375.15416.5144-0.5048-1.2796-1.08461.41990.4116-0.88431.03350.83630.23010.44160.0223-0.07480.40160.00610.701431.092338.542524.4438
83.9535-3.81020.54773.99850.54163.3327-0.1462-0.7279-0.8330.58910.08810.39240.3563-0.0884-0.13490.40630.06020.03350.17690.03010.532212.274638.865329.9899
92.8524-0.64783.09564.3756-4.80637.39310.42150.77040.237-0.29780.19060.756-0.54670.3205-0.49080.70330.1370.18310.4702-0.00030.491919.719929.61610.6758
106.3471.55581.19350.9323-0.89375.56910.1177-1.75960.39352.46780.38060.89390.7411-1.067-0.41081.3790.16950.43240.80660.08650.934711.426722.111439.3357
115.4242-1.3399-1.85081.00790.79590.8049-0.4082-2.5111-0.7051.98040.03780.23731.98770.36530.96461.706-0.01940.5121.13680.37011.06649.404919.956843.7955
128.1278-3.4594-1.33326.02682.11462.6601-0.26481.8078-0.3831-1.57270.1095-0.01650.2552-0.29650.20690.9167-0.21950.09590.566-0.06390.485620.346425.712913.8652
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 505 )
3X-RAY DIFFRACTION3chain 'A' and (resid 506 through 527 )
4X-RAY DIFFRACTION4chain 'A' and (resid 528 through 533 )
5X-RAY DIFFRACTION5chain 'A' and (resid 534 through 545 )
6X-RAY DIFFRACTION6chain 'A' and (resid 546 through 573 )
7X-RAY DIFFRACTION7chain 'A' and (resid 574 through 583 )
8X-RAY DIFFRACTION8chain 'A' and (resid 584 through 596 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 8 )
10X-RAY DIFFRACTION10chain 'D' and (resid 9 through 18 )
11X-RAY DIFFRACTION11chain 'E' and (resid 19 through 26 )
12X-RAY DIFFRACTION12chain 'E' and (resid 27 through 36 )

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