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- PDB-5kl7: Wilms Tumor Protein (WT1) ZnF2-4Q369R in complex with carboxylated DNA -

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Basic information

Entry
Database: PDB / ID: 5kl7
TitleWilms Tumor Protein (WT1) ZnF2-4Q369R 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 ...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 / 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 / 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 / negative regulation of translation / sequence-specific DNA binding / 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 / nucleolus / regulation of DNA-templated transcription / 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 / cytosol / cytoplasm
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: 1.579 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 / Derived calculations / Category: atom_site / struct_conn / 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)18,4008
Polymers18,0793
Non-polymers3205
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-4 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.458, 77.797, 35.683
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-645-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Wilms tumor protein / / WT33


Mass: 11311.947 Da / Num. of mol.: 1 / Fragment: UNP residues 333-420 / Mutation: Q369R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / Plasmid: pXC1302 / 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, 131 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 / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% (w/v) polyethylene glycol 3350, 40 mM citric acid, and 60 mM bistris-propane 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: Mar 8, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.579→30 Å / Num. obs: 26124 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.7
Reflection shellResolution: 1.579→1.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.81 / % possible all: 99.6

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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: 1.579→29.231 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 1304 5.01 %Random
Rwork0.1637 ---
obs0.1652 26017 98.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.579→29.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 449 11 126 1336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111366
X-RAY DIFFRACTIONf_angle_d1.3571930
X-RAY DIFFRACTIONf_dihedral_angle_d25.052757
X-RAY DIFFRACTIONf_chiral_restr0.064201
X-RAY DIFFRACTIONf_plane_restr0.009164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5788-1.6420.22161230.2082335X-RAY DIFFRACTION85
1.642-1.71670.20611450.17552743X-RAY DIFFRACTION99
1.7167-1.80720.18181450.16062734X-RAY DIFFRACTION99
1.8072-1.92040.1891440.16122755X-RAY DIFFRACTION100
1.9204-2.06870.20061470.16342771X-RAY DIFFRACTION100
2.0687-2.27680.15571460.15612780X-RAY DIFFRACTION100
2.2768-2.6060.1991480.15542815X-RAY DIFFRACTION100
2.606-3.28260.22041490.17062829X-RAY DIFFRACTION100
3.2826-29.23590.1861570.16092951X-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)
14.88760.63860.06054.7025-0.50294.0820.3065-0.19570.38620.6146-0.15370.1948-0.2107-0.1183-0.13410.21-0.03030.04350.1397-0.01740.1808-198.116-46.8499153.8973
23.07960.24141.08521.40840.97031.9929-0.03720.0835-0.44470.09190.1928-0.24260.07850.1313-0.17090.14840.02380.01610.1213-0.00930.2218-194.8421-67.2646143.9856
32.33810.49730.35773.41230.6892.3626-0.08670.5069-0.7109-0.2087-0.06020.18580.4766-0.48470.02940.1728-0.04930.03610.2378-0.07910.2635-213.7745-72.2729132.9461
46.90731.23610.50067.71270.79066.2793-0.04980.52540.441-0.4916-0.1908-0.0383-0.161-0.16410.13140.13110.03260.01180.20090.01140.1527-213.849-64.1762132.7401
51.8111.18470.97652.6924-0.82212.04060.0969-0.02650.07550.04430.12770.0746-0.0994-0.1914-0.22130.12750.0094-0.00210.14110.02030.1213-203.8358-58.6781144.166
62.24031.5479-0.72531.7461.2276.44990.3091-0.03980.16110.04440.14360.16330.0224-0.1657-0.38070.17450.01760.0210.1662-0.00660.1617-204.7833-59.3107145.5791
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 350 through 378 )
2X-RAY DIFFRACTION2chain 'A' and (resid 379 through 411 )
3X-RAY DIFFRACTION3chain 'A' and (resid 412 through 424 )
4X-RAY DIFFRACTION4chain 'A' and (resid 425 through 436 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 11 )

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