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- PDB-5kl5: Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with carboxylat... -

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Basic information

Entry
Database: PDB / ID: 5kl5
TitleWilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with carboxylated DNA
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(1CC)P*GP*T)-3')
  • DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
  • Wilms tumor protein
KeywordsTranscription/DNA / Wilms Tumor Protein / WT1 / zinc finger / 5-carboxyl cytosine / 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 / 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: 2.289 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 2.0Jun 24, 2020Group: Atomic model / Category: atom_site / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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*(1CC)P*GP*T)-3')
C: DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3197
Polymers18,0603
Non-polymers2584
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-7 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.493, 77.211, 35.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

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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 / Fragment: UNP residues 333-420 / Mutation: Q369H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / 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*(1CC)P*GP*T)-3')


Mass: 3474.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3293.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 90 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% (w/v) polyethylene glycol 3350, 0.2 M ammonium acetate, and 0.1 M bistris-HCl, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 17, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.289→30 Å / Num. obs: 8861 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 19.9
Reflection shellResolution: 2.289→2.37 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.76 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2400: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2R

4r2r


Resolution: 2.289→29.263 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 437 5.02 %random
Rwork0.1931 ---
obs0.1957 8708 97.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.289→29.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 449 7 86 1297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041297
X-RAY DIFFRACTIONf_angle_d0.6591814
X-RAY DIFFRACTIONf_dihedral_angle_d20.619700
X-RAY DIFFRACTIONf_chiral_restr0.036182
X-RAY DIFFRACTIONf_plane_restr0.003160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2891-2.62020.26521360.21992583X-RAY DIFFRACTION94
2.6202-3.30040.28591480.21182791X-RAY DIFFRACTION100
3.3004-29.26540.2231530.17662897X-RAY DIFFRACTION100
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)
12.1475-1.3983-0.21551.86380.56852.11120.16150.10010.3904-0.33360.0434-0.2012-0.1330.1849-0.18760.3114-0.0020.03750.3258-0.00580.3042266.3451-46.2075-100.787
21.48740.53920.5091.154-0.53951.161-0.01640.0538-0.1721-0.005-0.0039-0.06930.0519-0.01740.00490.2120.00910.02830.26190.00540.2636270.7054-67.0127-85.9231
32.4436-0.88391.31891.36110.0222.28-0.3609-0.1983-0.18910.15580.3315-0.1168-0.4302-0.36050.04120.3359-0.01270.0160.27670.01340.2698267.6298-60.1865-83.0661
40.4410.2635-0.03884.00932.70113.73740.1384-0.05640.4117-0.93190.8646-0.7806-0.36710.8074-0.79320.4277-0.06260.03140.5312-0.06380.3516275.6654-55.5626-99.7465
56.03431.12251.05741.7785-0.87744.80021.2963-0.9844-0.41510.946-0.00170.35740.1438-0.5404-0.75690.5739-0.0599-0.04570.40640.05990.3396267.8707-62.7306-104.4707
62.5407-0.3705-1.48622.52672.22814.97120.0197-0.38770.1122-0.04580.5387-0.0169-0.27210.7463-0.47850.38240.0172-0.01690.3458-0.02260.2936273.5944-56.5289-86.1999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 349:377)
2X-RAY DIFFRACTION2(chain A and resid 378:436)
3X-RAY DIFFRACTION3(chain B and resid 1:6)
4X-RAY DIFFRACTION4(chain B and resid 7:11)
5X-RAY DIFFRACTION5(chain C and resid 1:4)
6X-RAY DIFFRACTION6(chain C and resid 5:11)

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