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- PDB-2jp9: Structure of the Wilms Tumor Suppressor Protein Zinc Finger Domai... -

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Basic information

Entry
Database: PDB / ID: 2jp9
TitleStructure of the Wilms Tumor Suppressor Protein Zinc Finger Domain Bound to DNA
Components
  • DNA (5'-D(P*DCP*DGP*DCP*DGP*DGP*DGP*DGP*DGP*DCP*DGP*DTP*DCP*DTP*DGP*DCP*DGP*DC)-3')
  • DNA (5'-D(P*DGP*DCP*DGP*DCP*DAP*DGP*DAP*DCP*DGP*DCP*DCP*DCP*DCP*DCP*DGP*DCP*DG)-3')
  • Wilms tumor 1
KeywordsTRANSCRIPTION/DNA / DNA binding / nucleic acid recognition / residual dipolar coupling / zinc finger / Metal-binding / 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 / 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 / Wilms tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
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
DepositionApr 30, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: database_2 / ndb_struct_na_base_pair ...database_2 / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 ..._ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.tilt / _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(P*DCP*DGP*DCP*DGP*DGP*DGP*DGP*DGP*DCP*DGP*DTP*DCP*DTP*DGP*DCP*DGP*DC)-3')
C: DNA (5'-D(P*DGP*DCP*DGP*DCP*DAP*DGP*DAP*DCP*DGP*DCP*DCP*DCP*DCP*DCP*DGP*DCP*DG)-3')
A: Wilms tumor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1717
Polymers24,9093
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5690 Å2
ΔGint-42 kcal/mol
Surface area11740 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(P*DCP*DGP*DCP*DGP*DGP*DGP*DGP*DGP*DCP*DGP*DTP*DCP*DTP*DGP*DCP*DGP*DC)-3')


Mass: 5261.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*DGP*DCP*DGP*DCP*DAP*DGP*DAP*DCP*DGP*DCP*DCP*DCP*DCP*DCP*DGP*DCP*DG)-3')


Mass: 5159.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111filter-edit NOESY
121IPAP

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Sample preparation

DetailsContents: 0.6 mM [U-100% 13C; U-100% 15N] wt1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: wt1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20 / pH: 6.7 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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