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- PDB-3fkc: Crystal Structure of Human Zinc finger and BTB domain containing 33 -

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Basic information

Entry
Database: PDB / ID: 3fkc
TitleCrystal Structure of Human Zinc finger and BTB domain containing 33
ComponentsTranscriptional regulator Kaiso
KeywordsTRANSCRIPTION / Zinc finger and BTB domain containing 33 / Kaiso transcription factor / ZNF-kaiso / ZNF348 / WUGSC:H_DJ525N14.1 / Structural Genomics COnsortium / SGC / Activator / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Repressor / Transcription regulation / Wnt signaling pathway / Zinc-finger
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
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsFilippakopoulos, P. / Bullock, A. / Keates, T. / Burgess-Brown, N. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Filippakopoulos, P. / Bullock, A. / Keates, T. / Burgess-Brown, N. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of Human Zinc finger and BTB domain containing 33
Authors: Filippakopoulos, P. / Bullock, A. / Keates, T. / Burgess-Brown, N. / Muniz, J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S.
History
DepositionDec 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 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

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Assembly

Deposited unit
A: Transcriptional regulator Kaiso


Theoretical massNumber of molelcules
Total (without water)13,0691
Polymers13,0691
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transcriptional regulator Kaiso

A: Transcriptional regulator Kaiso


Theoretical massNumber of molelcules
Total (without water)26,1382
Polymers26,1382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area3440 Å2
ΔGint-24 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.358, 118.358, 38.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsGel filtration result shows that ZBTB33 construct is a monomer

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Components

#1: Protein Transcriptional regulator Kaiso / Zinc finger and BTB domain-containing protein 33


Mass: 13069.045 Da / Num. of mol.: 1 / Fragment: UNP residues 1-116, BTB domain / Mutation: E115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAISO, ZBTB33, ZNF348 / Plasmid: pNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86T24
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.8M (NH4)2SO4 0.1M citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.7→38.984 Å / Num. all: 18197 / Num. obs: 18142 / % possible obs: 99.7 % / Redundancy: 10.2 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 27.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 3 / Num. unique all: 2560 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 60.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.44 Å
Translation2.5 Å36.44 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.2data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2VKP,2IF5,2NN2,2IHC,1BUO,1CS3

2vkp

2if5

2nn2

2ihc

1buo

1cs3


Resolution: 1.7→38.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.885 / SU B: 3.815 / SU ML: 0.056 / SU R Cruickshank DPI: 0.091 / SU Rfree: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.195 926 5.1 %RANDOM
Rwork0.176 ---
all0.177 18205 --
obs0.177 18127 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 85 Å2 / Biso mean: 23.336 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0.32 Å20 Å2
2---0.63 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 0 122 1004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022944
X-RAY DIFFRACTIONr_bond_other_d0.0020.02638
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9721281
X-RAY DIFFRACTIONr_angle_other_deg0.99431569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2315114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73923.8142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36815180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.956156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
X-RAY DIFFRACTIONr_mcbond_it2.7163574
X-RAY DIFFRACTIONr_mcbond_other0.9073232
X-RAY DIFFRACTIONr_mcangle_it4.1055942
X-RAY DIFFRACTIONr_scbond_it6.5588370
X-RAY DIFFRACTIONr_scangle_it8.38511338
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 69 -
Rwork0.23 1220 -
all-1289 -
obs--100 %
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)
11.43530.52421.38660.79010.45672.7759-0.09330.18350.0524-0.06150.0659-0.0248-0.15580.2990.02740.03620.0070.01230.05760.01340.083528.29937.528413.8802
22.1012-0.36021.21871.63010.41413.50980.0241-0.0213-0.26330.04590.00670.18260.2645-0.1927-0.03080.0261-0.00980.00660.03510.00930.06638.852733.96295.3837
31.62330.13760.97961.4554-0.02571.1766-0.05290.24220.1667-0.16520.0134-0.0723-0.15540.07220.03950.0729-0.00230.01220.08010.0070.070513.090746.6637-1.4472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 33
2X-RAY DIFFRACTION2A34 - 71
3X-RAY DIFFRACTION3A72 - 117

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