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- PDB-2prt: Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domai... -

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Basic information

Entry
Database: PDB / ID: 2prt
TitleStructure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA
Components
  • DNA (5'-D(*CP*AP*GP*AP*CP*GP*CP*CP*CP*CP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*GP*GP*GP*GP*CP*GP*TP*CP*TP*G)-3')
  • Wilms tumor 1
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / 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 / mesenchymal to epithelial transition / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / 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 / 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 / sequence-specific DNA binding / negative regulation of translation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleolus / 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 / Wilms tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsStoll, R. / Lee, B.M. / Debler, E.W. / Laity, J.H. / Wilson, I.A. / Dyson, H.J. / Wright, P.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Wilms tumor suppressor protein zinc finger domain bound to DNA
Authors: Stoll, R. / Lee, B.M. / Debler, E.W. / Laity, J.H. / Wilson, I.A. / Dyson, H.J. / Wright, P.E.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*GP*CP*GP*GP*GP*GP*GP*CP*GP*TP*CP*TP*G)-3')
C: DNA (5'-D(*CP*AP*GP*AP*CP*GP*CP*CP*CP*CP*CP*GP*CP*G)-3')
A: Wilms tumor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3167
Polymers23,0543
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-17.3 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.879, 86.879, 171.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*GP*GP*GP*GP*GP*CP*GP*TP*CP*TP*G)-3')


Mass: 4353.801 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*GP*AP*CP*GP*CP*CP*CP*CP*CP*GP*CP*G)-3')


Mass: 4211.734 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Wilms tumor 1


Mass: 14488.708 Da / Num. of mol.: 1 / Fragment: residues 174-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VXV4, UniProt: P19544*PLUS
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 277 K / pH: 6.7
Details: 10 mM d11-Tris/HCl, 20 mM KCl, 5uM ZnSO4, 2mM NaN3, 10% D2O, pH 6.7, SMALL TUBES, temperature 277K, pH 6.70
Components of the solutions
IDNameCrystal-IDSol-ID
1d11-Tris/HCl11
2d11-Tris/HCl12
3KCl11
4KCl12
5ZnSO411
6ZnSO412
7NaN311
8NaN312

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.1921
DetectorDate: Feb 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1921 Å / Relative weight: 1
ReflectionResolution: 3.15→42.8 Å / Num. obs: 7166 / % possible obs: 99.1 % / Redundancy: 11.2 % / Rsym value: 0.085 / Net I/σ(I): 22.9
Reflection shellHighest resolution: 3.15 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.435 / % possible all: 100

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AAY

1aay


Highest resolution: 3.15 Å
RfactorNum. reflection
Rfree0.277 -
Rwork0.236 -
obs0.236 6530
Refinement stepCycle: LAST / Highest resolution: 3.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 526 4 0 1513
LS refinement shellHighest resolution: 3.15 Å / Rfactor Rfree: 0.405 / Rfactor Rwork: 0.376

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