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- PDB-1xf7: High Resolution NMR Structure of the Wilms' Tumor Suppressor Prot... -

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Basic information

Entry
Database: PDB / ID: 1xf7
TitleHigh Resolution NMR Structure of the Wilms' Tumor Suppressor Protein (WT1) Finger 3
ComponentsWilms' Tumor Protein
KeywordsTRANSCRIPTION / Zinc Finger
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 / 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 / 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 / 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 / regulation of DNA-templated transcription / nucleolus / 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 / cytoplasm / cytosol
Similarity search - Function
Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsLachenmann, M.J. / Ladbury, J.E. / Dong, J. / Huang, K. / Carey, P. / Weiss, M.A.
CitationJournal: Biochemistry / Year: 2004
Title: Why zinc fingers prefer zinc: ligand-field symmetry and the hidden thermodynamics of metal ion selectivity
Authors: Lachenmann, M.J. / Ladbury, J.E. / Dong, J. / Huang, K. / Carey, P. / Weiss, M.A.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wilms' Tumor Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5632
Polymers3,4981
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Wilms' Tumor Protein / WT33 / Wilms' Tumor Suppressor Protein


Mass: 3498.027 Da / Num. of mol.: 1 / Fragment: Zinc Finger 3 / Mutation: K28E; T29K / Source method: obtained synthetically
Details: SYNTHESIZED BY SOLID-PHASE SYNTHESIS. THE SEQUENCE OCCURS NATURALLY HOMO SAPIENS (HUMAN). THE G28E AND T29K MUTATIONS IMPROVE SAMPLE BEHAVIOR WITHOUT AFFECTING THE STRUCTURE
References: UniProt: P19544
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
111DQF-COSY
1212D NOESY
1312D TOCSY
1413D-TOCSY-NOESY
1512D-ROESY
162DQF-COSY
1722D NOESY
1822D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
15mM WT1-F3[EK]90% H2O/10% D2O
25mM WT1-F3[EK]100% D2O
Sample conditionsIonic strength: 50mM D11-TRIS-HCL, 5.5mM ZnCl2 / pH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS5001
Varian UNITYPLUSVarianUNITYPLUS5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.3-5.3Varian, Inc.processing
DGIIStandaloneHavel, T.F.structure solution
X-PLOR3.1Brunger, A.T.refinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 40

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