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- PDB-6b0r: Zinc finger Domain of WT1(-KTS form) with M342R Mutation and 14+1... -

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Basic information

Entry
Database: PDB / ID: 6b0r
TitleZinc finger Domain of WT1(-KTS form) with M342R Mutation and 14+1mer Oligonucleotide with 3' Triplet TGG
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*TP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*AP*CP*CP*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 / 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 / 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: 1.818 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(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*TP*TP*A)-3')
F: DNA (5'-D(P*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
A: Wilms tumor protein
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*TP*TP*A)-3')
C: DNA (5'-D(P*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,31316
Polymers47,6666
Non-polymers64710
Water3,261181
1
D: Wilms tumor protein
E: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*TP*TP*A)-3')
F: DNA (5'-D(P*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0957
Polymers23,8333
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-36 kcal/mol
Surface area11380 Å2
MethodPISA
2
A: Wilms tumor protein
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*TP*TP*A)-3')
C: DNA (5'-D(P*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2199
Polymers23,8333
Non-polymers3866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-27 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.940, 35.113, 87.148
Angle α, β, γ (deg.)90.00, 110.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules DA

#1: Protein Wilms tumor protein / WT33


Mass: 14652.923 Da / Num. of mol.: 2 / Fragment: UNP residues 304-420 / Mutation: M342R
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(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*TP*TP*A)-3')


Mass: 4730.069 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*AP*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 4449.901 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 191 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.: 181 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 2000 MME o.1M KCN

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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: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.818→31.35 Å / Num. obs: 39284 / % possible obs: 99.9 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.03 / Net I/σ(I): 21.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 3 / Num. unique obs: 3843 / CC1/2: 0.85 / Rpim(I) all: 0.301 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.818→31.321 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.28
RfactorNum. reflection% reflection
Rfree0.2335 3776 5.01 %
Rwork0.2079 --
obs0.2092 39284 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.818→31.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 1201 16 181 3362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033420
X-RAY DIFFRACTIONf_angle_d0.4634799
X-RAY DIFFRACTIONf_dihedral_angle_d21.7941371
X-RAY DIFFRACTIONf_chiral_restr0.031491
X-RAY DIFFRACTIONf_plane_restr0.003415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8184-1.84140.4595740.33941334X-RAY DIFFRACTION48
1.8414-1.86570.28611360.30952624X-RAY DIFFRACTION98
1.8657-1.89120.30411390.29852635X-RAY DIFFRACTION99
1.8912-1.91820.30751440.30932725X-RAY DIFFRACTION99
1.9182-1.94690.40721440.30992731X-RAY DIFFRACTION100
1.9469-1.97730.34741420.30392693X-RAY DIFFRACTION100
1.9773-2.00970.31471410.27882686X-RAY DIFFRACTION100
2.0097-2.04430.29021420.29412749X-RAY DIFFRACTION100
2.0443-2.08150.32331460.27362728X-RAY DIFFRACTION100
2.0815-2.12150.30121440.27072703X-RAY DIFFRACTION100
2.1215-2.16480.29031420.25882682X-RAY DIFFRACTION100
2.1648-2.21190.29741430.25042698X-RAY DIFFRACTION100
2.2119-2.26330.29751390.25152703X-RAY DIFFRACTION100
2.2633-2.31990.25441450.25142736X-RAY DIFFRACTION100
2.3199-2.38260.30421410.23352679X-RAY DIFFRACTION100
2.3826-2.45270.32811470.2472724X-RAY DIFFRACTION100
2.4527-2.53180.30211450.2542762X-RAY DIFFRACTION100
2.5318-2.62230.26861380.23172672X-RAY DIFFRACTION100
2.6223-2.72720.33261470.24882748X-RAY DIFFRACTION100
2.7272-2.85130.25831430.23632669X-RAY DIFFRACTION100
2.8513-3.00150.29011410.23882728X-RAY DIFFRACTION100
3.0015-3.18940.23121460.22792711X-RAY DIFFRACTION99
3.1894-3.43530.22131400.19392641X-RAY DIFFRACTION98
3.4353-3.78050.16571410.1782697X-RAY DIFFRACTION100
3.7805-4.32630.19861440.17022721X-RAY DIFFRACTION100
4.3263-5.44610.21311400.16262685X-RAY DIFFRACTION100
5.4461-31.32510.17841420.16812709X-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)
10.83060.36770.54940.6591-0.15920.552-0.12290.1171-0.13010.47110.03720.2174-0.2901-0.6391-0.00170.2832-0.02510.01970.43660.06830.4065-55.60884.293127.8613
22.1535-1.3567-1.32711.67390.51172.091-0.2155-0.0779-0.1099-0.12410.3949-0.08270.08450.30610.01840.2760.03160.03670.18320.01060.3149-30.63342.297730.274
30.2994-0.1699-0.27440.08540.13910.4339-0.0443-0.79660.1199-0.08110.2249-0.0410.18210.711100.42350.0710.05930.5169-0.05410.368-35.994115.569352.6032
42.4351-0.9926-1.96673.40911.05421.51220.08040.0142-0.37980.06070.34380.24610.2305-0.05940.1230.25210.03950.00160.24390.03290.1597-36.51767.233532.5845
51.805-0.9168-0.74641.87250.37773.66710.0107-0.0697-0.09070.26310.36490.1088-0.16640.73910.5480.28630.071-0.05340.21110.09730.2741-38.08754.638931.8586
60.2922-0.10780.23110.2169-0.58621.51510.0389-0.5449-1.1137-0.42080.2566-0.4055-0.3211.34040.13280.4479-0.04760.03640.8424-0.08010.61776.508-5.048211.2995
70.06240.0665-0.07540.0709-0.0580.025-0.1494-0.21370.1062-0.2178-0.0621-0.6039-0.29311.221900.4489-0.07150.00520.7886-0.01160.40333.112-4.414510.1198
80.0897-0.0614-0.41770.10220.24342.4407-0.0531-1.451-0.2984-0.103-0.0804-0.3958-0.20080.96110.01020.32670.1188-0.01020.6460.07540.4605-2.0171-7.575917.125
91.48140.14760.36460.57241.08672.2811-0.9562-0.4463-0.99370.1146-0.22270.01590.84760.0752-0.34830.45270.13330.15650.31240.20350.6089-19.1139-13.927321.881
101.89751.53930.58082.0257-0.50792.6291-0.3828-0.061-1.4154-0.0329-0.1875-0.06150.440.3016-0.59310.47060.08870.14370.3832-0.06260.8637-17.3964-13.494517.7651
110.43710.1719-0.60290.3713-0.31550.78040.05170.01730.26960.35830.0708-0.2294-0.3025-0.078400.33180.04210.05460.25390.00890.3561-25.208-1.182914.0428
120.67450.05610.45670.4096-0.32280.36750.3550.6880.4041-0.10920.3901-0.1573-0.3461-0.73570.05550.40120.10150.12210.47860.13140.4081-21.71623.3236-4.9179
130.03650.02860.09680.30790.08210.26730.0387-0.5686-0.02950.7323-0.22580.03440.8872-0.2083-0.00090.4425-0.01310.06020.6248-0.12420.4229-16.5608-6.9157-11.7026
143.0719-0.3203-2.41861.5406-0.64271.92580.0219-0.2086-0.18470.07950.3158-0.2488-0.2952-0.46610.03680.36460.009-0.01560.3733-0.06260.2792-15.9643-0.93927.8602
151.93350.5067-1.30391.7509-0.83580.88610.1326-0.0914-0.16170.0513-0.0024-0.1935-0.32170.00540.00530.3125-0.06970.00620.4585-0.06630.3356-14.2322-2.545310.3495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 320 through 348 )
2X-RAY DIFFRACTION2chain 'D' and (resid 349 through 411 )
3X-RAY DIFFRACTION3chain 'D' and (resid 412 through 436 )
4X-RAY DIFFRACTION4chain 'E' and (resid 1 through 15 )
5X-RAY DIFFRACTION5chain 'F' and (resid 2 through 15 )
6X-RAY DIFFRACTION6chain 'A' and (resid 319 through 328 )
7X-RAY DIFFRACTION7chain 'A' and (resid 329 through 336 )
8X-RAY DIFFRACTION8chain 'A' and (resid 337 through 348 )
9X-RAY DIFFRACTION9chain 'A' and (resid 349 through 358 )
10X-RAY DIFFRACTION10chain 'A' and (resid 359 through 366 )
11X-RAY DIFFRACTION11chain 'A' and (resid 367 through 388 )
12X-RAY DIFFRACTION12chain 'A' and (resid 389 through 424 )
13X-RAY DIFFRACTION13chain 'A' and (resid 425 through 436 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1 through 15 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 15 )

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