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- PDB-6b0p: Zinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide... -

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Basic information

Entry
Database: PDB / ID: 6b0p
TitleZinc finger Domain of WT1(-KTS form) with 12+1mer Oligonucleotide with 3' Triplet GGT
Components
  • DNA (5'-D(P*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*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 / 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: 2.077 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*GP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*CP*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*GP*GP*T)-3')
C: DNA (5'-D(P*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,79216
Polymers45,1446
Non-polymers64710
Water5,819323
1
D: Wilms tumor protein
E: DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*T)-3')
F: DNA (5'-D(P*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8347
Polymers22,5723
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-25 kcal/mol
Surface area10760 Å2
MethodPISA
2
A: Wilms tumor protein
B: DNA (5'-D(P*GP*CP*GP*TP*GP*GP*GP*AP*GP*GP*GP*T)-3')
C: DNA (5'-D(P*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9589
Polymers22,5723
Non-polymers3866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-17 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.798, 84.402, 85.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 / 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 EBFC

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


Mass: 4112.669 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*CP*CP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3832.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 333 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.: 323 / 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: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 20% PEG 3350 0.03M Citric Acid 0.07M BiS-TRIS Propane

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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: 2.077→37.883 Å / Num. obs: 33923 / % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.043 / Net I/σ(I): 17.5
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3354 / CC1/2: 0.851 / Rpim(I) all: 0.322 / % 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: 2.077→37.883 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2261 3201 5 %
Rwork0.1877 --
obs0.1896 33860 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.077→37.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 984 16 323 3320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033197
X-RAY DIFFRACTIONf_angle_d0.5294493
X-RAY DIFFRACTIONf_dihedral_angle_d17.8481766
X-RAY DIFFRACTIONf_chiral_restr0.036456
X-RAY DIFFRACTIONf_plane_restr0.003413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0768-2.10780.31171320.2962536X-RAY DIFFRACTION95
2.1078-2.14080.33721370.25822617X-RAY DIFFRACTION100
2.1408-2.17590.29921390.26782673X-RAY DIFFRACTION100
2.1759-2.21340.28741410.26362642X-RAY DIFFRACTION100
2.2134-2.25360.28641420.26272651X-RAY DIFFRACTION100
2.2536-2.2970.321390.24822676X-RAY DIFFRACTION100
2.297-2.34380.32111390.2322603X-RAY DIFFRACTION100
2.3438-2.39480.25391420.22952664X-RAY DIFFRACTION100
2.3948-2.45050.29661390.21992707X-RAY DIFFRACTION100
2.4505-2.51180.24351320.21132631X-RAY DIFFRACTION100
2.5118-2.57960.23791430.21292652X-RAY DIFFRACTION100
2.5796-2.65550.24391400.20882630X-RAY DIFFRACTION100
2.6555-2.74120.24161390.19542680X-RAY DIFFRACTION100
2.7412-2.83920.24251500.20642639X-RAY DIFFRACTION100
2.8392-2.95280.31151350.20872664X-RAY DIFFRACTION100
2.9528-3.08710.22661450.20422658X-RAY DIFFRACTION100
3.0871-3.24980.24811410.19172631X-RAY DIFFRACTION99
3.2498-3.45330.20031430.17292655X-RAY DIFFRACTION99
3.4533-3.71970.18821390.1522614X-RAY DIFFRACTION99
3.7197-4.09360.2111350.16062676X-RAY DIFFRACTION100
4.0936-4.68510.18931400.15662652X-RAY DIFFRACTION100
4.6851-5.89910.18051280.13912664X-RAY DIFFRACTION100
5.8991-37.8890.15981410.15612650X-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)
18.1774-0.88255.50031.1832-1.12214.0830.3050.73240.48640.012-0.4461-0.22960.51140.75320.17810.3259-0.0077-0.05290.4070.13430.4065-10.863333.651-59.3131
28.5501-0.9525-0.9055.62910.01335.08160.10880.71310.1380.1196-0.1060.69350.07350.00010.12630.26580.0052-0.04990.31720.1380.4822-11.167531.318-52.8866
34.35261.16871.61963.6820.18228.39740.6118-0.74280.67490.6821-0.1781-0.2309-1.1981.4976-0.34880.5193-0.25740.01180.6233-0.05730.3426-7.396529.3568-34.0589
47.10353.07-2.61278.807-4.52127.34410.3388-0.39640.63370.8752-0.21720.7715-1.46550.1225-0.14480.448-0.01320.01230.244-0.05560.3385-15.851825.6278-31.4235
59.01253.33310.10934.0820.36985.6012-0.1117-0.71270.40540.7343-0.07750.80580.0234-0.55350.13880.31220.10780.11210.33740.02930.3422-30.371715.8429-29.2819
63.78873.3414-3.33543.3486-2.16326.7279-0.0223-0.0892-0.1470.22120.25250.49860.2916-0.7376-0.22420.25020.02940.00810.33550.11730.3891-27.855812.5422-34.8492
70.81850.160.30641.39130.61490.89180.27770.26650.499-0.245-0.07220.7816-0.3333-0.1352-0.11120.32790.0546-0.00960.32670.19170.5762-20.360628.3641-43.4479
81.3146-1.50010.35056.877-3.93153.46630.39790.29740.35470.1551-0.31130.2935-0.4628-0.0087-0.14420.40680.04630.03320.32780.10130.4775-19.431927.2931-43.9931
90.31370.01930.38350.0809-0.1513.67520.0653-0.4858-0.59660.3088-0.346-0.21460.01750.372-0.24450.2485-0.00110.00890.30210.1230.4044-5.6697-7.4426-11.9275
105.39323.7933-2.01163.7556-0.54644.35630.0224-0.4301-0.30720.184-0.057-0.0445-0.0716-0.0070.05930.1851-0.0032-0.00110.16610.05630.2073-11.1907-3.0984-13.4516
117.171-4.2235-4.28762.67432.65662.68110.59971.1435-0.4366-0.194-0.50380.2647-0.2364-0.9331-0.04050.24910.0346-0.03690.38930.01730.2842-26.498.0668-16.7056
125.2954-1.7423-1.74956.29623.01925.76890.30680.1853-0.09770.1169-0.3824-0.3193-0.2144-0.1572-0.01540.2982-0.03770.03310.2187-0.00540.3252-25.72379.8816-9.8667
131.35030.4119-2.66431.86210.2015.89120.0558-0.6598-0.30310.413-0.11960.35980.8109-0.9350.18150.4171-0.13540.07020.64240.02140.2298-29.116511.07028.7217
144.84961.4517-0.24994.76591.03739.5426-0.0099-1.0691-0.40660.486-0.0121-0.23820.4905-0.0897-0.06310.38120.00320.06080.4060.05050.2677-20.553414.610511.418
158.31924.38651.08285.42340.55253.90640.3363-1.304-0.18720.6147-0.3614-0.58070.12150.55210.01870.35480.0602-0.03020.5324-0.05290.3197-7.896226.054513.5593
167.68933.09884.66918.35712.9636.7055-0.32170.80690.2064-0.31920.3537-0.3863-0.01770.76840.06370.25610.05530.02070.3887-0.06340.3332-8.583829.11775.0104
170.93370.04551.01933.3292-0.97361.26930.33590.0489-0.2206-0.5169-0.3829-0.36420.15430.08230.03520.27620.02540.04740.2579-0.03540.2893-16.841212.6676-0.2335
183.3277-2.7134-0.50833.30762.44083.31430.2894-0.23680.19420.0856-0.2861-0.42290.1298-0.1442-0.03630.32830.01420.03760.3114-0.02160.2428-17.627713.3748-1.1854
193.68142.49511.36734.63111.48854.44480.0476-0.20550.63760.3561-0.21350.45730.0364-0.2241-0.07720.1788-0.00170.02190.2515-0.02670.3162-32.558846.4484-54.773
202.323.75373.14889.16724.00085.22140.096-0.13870.03310.24310.0144-0.3140.20130.0863-0.21040.1353-0.0011-0.00940.1427-0.02120.2079-26.620342.8875-56.2842
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 349 through 358 )
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 378 )
3X-RAY DIFFRACTION3chain 'A' and (resid 379 through 394 )
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 406 )
5X-RAY DIFFRACTION5chain 'A' and (resid 407 through 416 )
6X-RAY DIFFRACTION6chain 'A' and (resid 417 through 436 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 13 )
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 13 )
9X-RAY DIFFRACTION9chain 'D' and (resid 319 through 328 )
10X-RAY DIFFRACTION10chain 'D' and (resid 329 through 348 )
11X-RAY DIFFRACTION11chain 'D' and (resid 349 through 358 )
12X-RAY DIFFRACTION12chain 'D' and (resid 359 through 378 )
13X-RAY DIFFRACTION13chain 'D' and (resid 379 through 394 )
14X-RAY DIFFRACTION14chain 'D' and (resid 395 through 406 )
15X-RAY DIFFRACTION15chain 'D' and (resid 407 through 424 )
16X-RAY DIFFRACTION16chain 'D' and (resid 425 through 436 )
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 13 )
18X-RAY DIFFRACTION18chain 'F' and (resid 2 through 13 )
19X-RAY DIFFRACTION19chain 'A' and (resid 319 through 328 )
20X-RAY DIFFRACTION20chain 'A' and (resid 329 through 348 )

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