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- PDB-5kl2: Wilms Tumor Protein (WT1) ZnF2-4 in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5kl2
TitleWilms Tumor Protein (WT1) ZnF2-4 in complex with DNA
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*AP*GP*T)-3')
  • DNA (5'-D(*TP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')
  • Wilms tumor protein
KeywordsTRANSCRIPTION/DNA / Wilms Tumor Protein / WT1 / zinc finger / 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 / 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: 1.692 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 1.5Sep 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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


Theoretical massNumber of molelcules
Total (without water)18,52112
Polymers17,9913
Non-polymers5309
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-13 kcal/mol
Surface area8340 Å2
Unit cell
Length a, b, c (Å)70.107, 65.089, 35.702
Angle α, β, γ (deg.)90.00, 93.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Wilms tumor protein / WT33


Mass: 11282.882 Da / Num. of mol.: 1 / Fragment: UNP residues 333-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / Plasmid: pXC1295 / 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*AP*GP*T)-3')


Mass: 3454.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*CP*TP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3254.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 116 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 16% (w/v) PEG 3350, 20 mM Citric acid, 80 mM Bis-tris propane, pH 8.8

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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 9, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→30 Å / Num. obs: 17475 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 16.3
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.9 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX(dev_2439: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2R

4r2r


Resolution: 1.692→29.115 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.21
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 870 5 %Random
Rwork0.1641 ---
obs0.1656 17401 97.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.692→29.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms753 445 24 107 1329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131332
X-RAY DIFFRACTIONf_angle_d1.1941857
X-RAY DIFFRACTIONf_dihedral_angle_d19.162725
X-RAY DIFFRACTIONf_chiral_restr0.065191
X-RAY DIFFRACTIONf_plane_restr0.009162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6922-1.79820.2611180.24182423X-RAY DIFFRACTION85
1.7982-1.9370.20711460.20882766X-RAY DIFFRACTION98
1.937-2.13190.21081460.18142821X-RAY DIFFRACTION100
2.1319-2.44020.18981500.16762835X-RAY DIFFRACTION100
2.4402-3.07390.22611550.16742837X-RAY DIFFRACTION100
3.0739-29.11920.16381550.14172849X-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)
12.13013.5816-3.08176.0262-5.22784.9956-0.09470.1111-1.3685-0.06180.3067-1.17590.90771.3454-0.0590.32050.0687-0.01810.4324-0.09670.404-34.796-265.3812-66.6261
22.48944.52872.65238.41164.07226.13580.11260.4176-0.55080.11220.2444-0.6370.02770.8079-0.40930.17970.02330.00680.3181-0.04430.2323-33.6893-259.163-60.9608
36.7793-1.3206-3.03362.60781.12943.56920.10740.18460.5101-0.10740.0360.0486-0.1945-0.0433-0.13270.1599-0.0072-0.02140.14160.02410.1855-48.3169-251.6253-58.2042
43.4139-0.0681-5.15984.8-0.62558.10210.0930.03030.13220.24970.1590.2204-0.214-0.0516-0.2240.14410.009400.1781-0.0060.1641-59.3718-255.802-52.5434
55.1854-5.3328-4.51927.82664.82174.20310.13570.43630.1364-0.4353-0.20111.3534-0.0967-0.791-0.01910.18320.0063-0.02140.24720.06360.3364-65.3826-263.8032-49.294
62.1302-2.27382.0434.4863-4.47164.53760.2786-0.2722-0.6590.5236-0.34780.68030.77220.16220.18060.4207-0.0570.02110.25850.00870.3043-64.4225-277.481-44.9309
72.3582.3362-3.26653.1742-3.60054.6993-0.0793-0.18320.03920.51740.20310.48780.3706-0.1423-0.10670.3154-0.01360.04090.24410.04620.2967-64.7243-269.4186-43.6319
85.71973.2988-0.24492.73020.63741.3721-0.1524-0.3595-0.27010.622-0.0283-0.37160.39940.45710.23170.3350.0852-0.01930.24860.02420.2064-56.6462-273.3107-42.8749
92.1035-0.1756-0.37481.9570.25373.61910.0307-0.1420.04390.11880.18210.00820.0563-0.2539-0.16470.13850.0047-0.01840.19430.04420.1323-50.6507-262.8058-52.7566
103.55380.64261.84022.6440.48778.70020.2281-0.0891-0.1807-0.02890.2022-0.07570.0779-0.0971-0.38790.1246-0.00250.02490.1683-0.02970.1813-50.3791-263.5002-55.3762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 350 through 354 )
2X-RAY DIFFRACTION2chain 'A' and (resid 355 through 366 )
3X-RAY DIFFRACTION3chain 'A' and (resid 367 through 394 )
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 406 )
5X-RAY DIFFRACTION5chain 'A' and (resid 407 through 411 )
6X-RAY DIFFRACTION6chain 'A' and (resid 412 through 416 )
7X-RAY DIFFRACTION7chain 'A' and (resid 417 through 424 )
8X-RAY DIFFRACTION8chain 'A' and (resid 425 through 437 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 11 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 11 )

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