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- PDB-6b0o: Zinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide... -

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Basic information

Entry
Database: PDB / ID: 6b0o
TitleZinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide with 3' Triplet TGT
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*T)-3')
  • DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
  • Wilms tumor protein
KeywordsTRANSCRIPTION/DNA / protein-DNA complex Wilms tumor suppressor protein zinc-fingers / 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 / positive regulation of male gonad development / cellular response to gonadotropin stimulus / gonad development / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / Transcriptional regulation of testis differentiation / tissue development / podocyte differentiation / double-stranded methylated DNA binding / cardiac muscle cell fate commitment / hemi-methylated DNA-binding / mesenchymal to epithelial transition / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / adrenal gland development / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / germ cell development / vasculogenesis / epithelial cell differentiation / RNA splicing / cellular response to cAMP / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / negative regulation of translation / nuclear speck / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Wilms tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Role for first zinc finger of WT1 in DNA sequence specificity: Denys-Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites.
Authors: Wang, D. / Horton, J.R. / Zheng, Y. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionSep 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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*TP*GP*T)-3')
C: DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
D: Wilms tumor protein
E: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*T)-3')
F: DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,79016
Polymers45,1426
Non-polymers64710
Water6,521362
1
A: Wilms tumor protein
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*T)-3')
C: DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9579
Polymers22,5713
Non-polymers3866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-19 kcal/mol
Surface area10900 Å2
MethodPISA
2
D: Wilms tumor protein
E: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*T)-3')
F: DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8337
Polymers22,5713
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-18 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.927, 42.657, 71.821
Angle α, β, γ (deg.)88.28, 77.71, 85.81
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Wilms tumor protein / WT33


Mass: 14626.925 Da / Num. of mol.: 2 / Fragment: UNP residues 304-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P19544

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DNA chain , 2 types, 4 molecules BECF

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


Mass: 4087.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3856.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 372 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350 0.2M Ammonium Acetate 0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→29.59 Å / Num. obs: 59787 / % possible obs: 96.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.028 / Net I/σ(I): 19.1
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5883 / CC1/2: 0.793 / Rpim(I) all: 0.327 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kl2

5kl2


Resolution: 1.552→29.588 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2062 3935 3.32 %
Rwork0.1928 --
obs0.1933 118578 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.552→29.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 1054 16 362 3374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033220
X-RAY DIFFRACTIONf_angle_d0.5284553
X-RAY DIFFRACTIONf_dihedral_angle_d18.2951765
X-RAY DIFFRACTIONf_chiral_restr0.033471
X-RAY DIFFRACTIONf_plane_restr0.003407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5517-1.57060.31941290.30633993X-RAY DIFFRACTION93
1.5706-1.59050.28321520.29064076X-RAY DIFFRACTION94
1.5905-1.61140.33641400.28883969X-RAY DIFFRACTION95
1.6114-1.63350.29191250.2584088X-RAY DIFFRACTION94
1.6335-1.65680.30151400.24714012X-RAY DIFFRACTION95
1.6568-1.68150.27371370.24394063X-RAY DIFFRACTION95
1.6815-1.70780.27981490.23534010X-RAY DIFFRACTION94
1.7078-1.73580.22811490.22753961X-RAY DIFFRACTION94
1.7358-1.76570.22751290.22834180X-RAY DIFFRACTION95
1.7657-1.79780.24971280.2264038X-RAY DIFFRACTION96
1.7978-1.83240.25111480.21444068X-RAY DIFFRACTION96
1.8324-1.86980.22411340.2174109X-RAY DIFFRACTION96
1.8698-1.91050.21071410.22453991X-RAY DIFFRACTION95
1.9105-1.95490.24861190.22554149X-RAY DIFFRACTION95
1.9549-2.00380.20281490.21874057X-RAY DIFFRACTION96
2.0038-2.05790.20361350.21884129X-RAY DIFFRACTION97
2.0579-2.11850.22921400.21214078X-RAY DIFFRACTION95
2.1185-2.18680.23581520.20554125X-RAY DIFFRACTION97
2.1868-2.2650.20431270.20854135X-RAY DIFFRACTION96
2.265-2.35560.23131550.20534138X-RAY DIFFRACTION97
2.3556-2.46280.20671320.20724161X-RAY DIFFRACTION97
2.4628-2.59260.24321510.20344062X-RAY DIFFRACTION97
2.5926-2.75490.19751430.20894206X-RAY DIFFRACTION97
2.7549-2.96740.24621380.20794145X-RAY DIFFRACTION98
2.9674-3.26570.19821490.19734212X-RAY DIFFRACTION98
3.2657-3.73740.1921420.1694075X-RAY DIFFRACTION97
3.7374-4.70570.15931460.14894217X-RAY DIFFRACTION98
4.7057-29.59330.15841560.14854196X-RAY DIFFRACTION99

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