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- PDB-5kl3: Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5kl3
TitleWilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with DNA
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*T)-3')
  • DNA (5'-D(*TP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
  • Wilms tumor protein
KeywordsTRANSCRIPTION/DNA / Wilms Tumor Protein / WT1 / zinc finger / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development ...posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development / Nephron development / glomerular basement membrane development / diaphragm development / sex determination / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / mesenchymal to epithelial transition / positive regulation of male gonad development / cellular response to gonadotropin stimulus / gonad development / Transcriptional regulation of testis differentiation / podocyte differentiation / cardiac muscle cell fate commitment / double-stranded methylated DNA binding / tissue development / hemi-methylated DNA-binding / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / negative regulation of gene expression via chromosomal CpG island methylation / adrenal gland development / branching involved in ureteric bud morphogenesis / germ cell development / vasculogenesis / cellular response to cAMP / epithelial cell differentiation / RNA splicing / kidney development / negative regulation of cell growth / positive regulation of miRNA transcription / male gonad development / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / negative regulation of translation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Wilm's tumour protein, N-terminal / Wilm's tumour protein / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...Wilm's tumour protein, N-terminal / Wilm's tumour protein / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Wilms tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å
AuthorsHashimoto, H. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications.
Authors: Hashimoto, H. / Zhang, X. / Zheng, Y. / Wilson, G.G. / Cheng, X.
History
DepositionJun 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wilms tumor protein
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*T)-3')
C: DNA (5'-D(*TP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2607
Polymers18,0013
Non-polymers2584
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-17 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.223, 66.069, 35.646
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Wilms tumor protein / WT33


Mass: 11292.900 Da / Num. of mol.: 1 / Mutation: Q369H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / Variant: -KTS / Plasmid: pXC1305 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL-codon plus / References: UniProt: P19544

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*T)-3')


Mass: 3454.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3254.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 184 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 12% (w/v) PEG 3350, 4% (v/v) Tacsimate, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 9, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.449→30 Å / Num. obs: 27228 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.3
Reflection shellResolution: 1.449→1.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / % possible all: 43.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2R

4r2r


Resolution: 1.449→29.223 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.25
RfactorNum. reflection% reflectionSelection details
Rfree0.1823 1361 5.01 %Random
Rwork0.1624 ---
obs0.1634 27162 87.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.449→29.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 445 7 180 1377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091313
X-RAY DIFFRACTIONf_angle_d1.1331846
X-RAY DIFFRACTIONf_dihedral_angle_d22.014544
X-RAY DIFFRACTIONf_chiral_restr0.069191
X-RAY DIFFRACTIONf_plane_restr0.01161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4494-1.50120.289990.27771223X-RAY DIFFRACTION43
1.5012-1.56130.3202620.23051961X-RAY DIFFRACTION65
1.5613-1.63230.28221080.20682338X-RAY DIFFRACTION79
1.6323-1.71840.19871450.19382686X-RAY DIFFRACTION92
1.7184-1.8260.20051560.17932883X-RAY DIFFRACTION98
1.826-1.9670.21981760.17342904X-RAY DIFFRACTION100
1.967-2.16490.1881810.17012903X-RAY DIFFRACTION100
2.1649-2.4780.19621620.15422932X-RAY DIFFRACTION100
2.478-3.12140.18841370.16922981X-RAY DIFFRACTION100
3.1214-29.22940.14461350.14112990X-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)
16.4022.23831.67675.16375.18018.6613-0.27320.0693-0.9743-0.34390.1662-1.1099-0.09910.4302-0.21590.268-0.0280.06440.2795-0.04070.3408-37.5781-261.8593-64.5254
26.1595.53956.78645.0786.15118.6180.25930.2875-1.57040.02880.4103-1.13620.58050.5932-0.53920.32860.0387-0.00880.2923-0.03020.4205-41.0823-267.6762-64.1097
33.67223.90242.76116.15266.29587.9193-0.0720.0963-0.14320.00210.1867-0.20840.02540.2235-0.07590.27330.00680.01840.19690.00390.1583-46.7977-260.573-62.7407
45.5660.0782-2.94063.6518-0.30122.82670.0130.12140.2057-0.0630.07490.3619-0.0887-0.0379-0.08570.16020.0134-0.0310.10680.01210.096-61.8157-257.0362-55.3444
54.91542.1491-1.70563.6349-1.34334.4821-0.1369-0.16150.0153-0.1728-0.12740.54150.0447-0.37830.16660.2120.0105-0.01160.1857-0.01660.1476-69.9744-275.4396-45.1545
62.66593.6716-2.45445.3805-3.51392.4216-0.1339-0.1527-0.1384-0.004-0.0534-0.42240.06360.05220.08540.34250.00540.00280.1768-0.00710.1492-61.6764-278.0428-43.2893
71.24570.46910.52421.3202-0.61840.83450.04590.0093-0.02450.10490.0898-0.07970.256-0.0549-0.08940.2610.0027-0.01860.1506-0.00190.1051-55.1574-268.2969-54.6526
81.69790.59480.3931.80120.18575.71680.1349-0.1111-0.0196-0.05450.2025-0.00460.1453-0.2909-0.31510.30360.01710.010.1791-0.02870.133-55.9087-268.5544-56.5158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 351 through 360 )
2X-RAY DIFFRACTION2chain 'A' and (resid 361 through 366 )
3X-RAY DIFFRACTION3chain 'A' and (resid 367 through 378 )
4X-RAY DIFFRACTION4chain 'A' and (resid 379 through 406 )
5X-RAY DIFFRACTION5chain 'A' and (resid 407 through 424 )
6X-RAY DIFFRACTION6chain 'A' and (resid 425 through 437 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 11 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 11 )

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