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- PDB-6b0q: Zinc finger Domain of WT1(-KTS form) with 13+1mer Oligonucleotide... -

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Basic information

Entry
Database: PDB / ID: 6b0q
TitleZinc finger Domain of WT1(-KTS form) with 13+1mer Oligonucleotide with 3' Triplet TGT
Components
  • DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-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 / mesenchymal to epithelial transition / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / positive regulation of male gonad development / cellular response to gonadotropin stimulus / Transcriptional regulation of testis differentiation / gonad development / podocyte differentiation / cardiac muscle cell fate commitment / double-stranded methylated DNA binding / hemi-methylated DNA-binding / tissue development / 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 / branching involved in ureteric bud morphogenesis / adrenal gland development / 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 / 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 / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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 / 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: 2.794 Å
AuthorsHorton, J.R. / Cheng, X.
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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
D: Wilms tumor protein
E: DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
A: Wilms tumor protein
B: DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3')
C: DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,66922
Polymers46,3776
Non-polymers1,29216
Water54030
1
D: Wilms tumor protein
E: DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,83411
Polymers23,1893
Non-polymers6468
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-62 kcal/mol
Surface area11860 Å2
MethodPISA
2
A: Wilms tumor protein
B: DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*TP*GP*TP*T)-3')
C: DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,83411
Polymers23,1893
Non-polymers6468
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-82 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.664, 161.664, 42.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules DA

#1: Protein Wilms tumor protein / WT33


Mass: 14626.925 Da / Num. of mol.: 2
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 EBFC

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


Mass: 4391.849 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*AP*CP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 4169.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 46 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350 0.2M Lithium Sulfate 0.1M BIS-TRIS

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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 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→38.83 Å / Num. obs: 30219 / % possible obs: 99.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.051 / Net I/σ(I): 13.5
Reflection shellResolution: 2.68→2.79 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 2 / Num. unique obs: 1516 / CC1/2: 0.686 / Rpim(I) all: 0.394 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.794→38.83 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1509 4.99 %
Rwork0.2254 --
obs0.2262 30219 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.794→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 1066 48 30 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043289
X-RAY DIFFRACTIONf_angle_d0.4794598
X-RAY DIFFRACTIONf_dihedral_angle_d20.7621759
X-RAY DIFFRACTIONf_chiral_restr0.031467
X-RAY DIFFRACTIONf_plane_restr0.003407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7938-2.8840.37351280.3392589X-RAY DIFFRACTION99
2.884-2.9870.41431400.32992689X-RAY DIFFRACTION100
2.987-3.10660.32921360.33482597X-RAY DIFFRACTION100
3.1066-3.24790.24921380.30142597X-RAY DIFFRACTION98
3.2479-3.4190.35711280.29012494X-RAY DIFFRACTION95
3.419-3.63310.30611340.24712567X-RAY DIFFRACTION98
3.6331-3.91340.25841440.2122634X-RAY DIFFRACTION100
3.9134-4.30670.21151460.19282633X-RAY DIFFRACTION100
4.3067-4.92890.1721430.17232651X-RAY DIFFRACTION100
4.9289-6.20580.16611370.16762633X-RAY DIFFRACTION100
6.2058-38.83420.18391350.18062626X-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)
12.0088-0.4788-0.67875.37530.7267.1764-0.7038-0.80521.10880.72660.377-0.0782-0.9425-0.90070.38860.54310.1242-0.1250.6882-0.01920.541284.486621.5915-32.9613
22.47370.7616-0.65614.1111-2.17864.0190.00130.0117-0.0692-0.00310.16170.20670.3474-0.2613-0.12160.38820.016-0.02190.1658-0.00720.271461.06059.7207-2.2524
31.112-0.5733-0.2421.9218-0.07732.1873-0.00120.1208-0.08530.01120.1720.2710.2528-0.3466-0.15610.4634-0.01470.01540.24850.03870.252461.58267.7622-7.4844
42.5174-0.4056-0.27972.3032-0.78886.8776-0.00750.09420.2604-0.18750.51720.1194-1.28660.0136-0.46040.6724-0.06840.05620.3542-0.00160.324663.35358.9658-7.4009
55.13772.7456-0.10884.6421-1.45594.35290.0332-0.79570.1268-0.0263-0.2340.6867-0.00440.31150.21160.43990.05690.09260.4395-0.01940.471352.603160.49110.3255
62.853-0.41961.39133.2545-0.3732.65270.1428-0.0827-0.18590.00840.03710.17710.0588-0.313-0.17370.33360.06620.06440.27820.04280.296550.460535.4466-19.8952
71.4666-0.68030.48742.27130.04661.94620.1928-0.2109-0.16590.04580.07290.1887-0.3001-0.7425-0.22550.40030.1112-0.02620.48740.08360.310749.792137.1232-13.7818
81.2018-0.57-0.64430.33890.4086.76750.43980.13580.13240.01350.3524-0.02190.3244-0.2561-0.75470.49880.1129-0.04620.45890.0760.358851.575137.2597-14.4322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 319 through 347 )
2X-RAY DIFFRACTION2chain 'D' and (resid 348 through 436 )
3X-RAY DIFFRACTION3chain 'E' and (resid 2 through 14 )
4X-RAY DIFFRACTION4chain 'F' and (resid 1 through 13 )
5X-RAY DIFFRACTION5chain 'A' and (resid 319 through 346 )
6X-RAY DIFFRACTION6chain 'A' and (resid 347 through 437 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 14 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 14 )

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