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- PDB-6wlh: RNA complex of WT1 zinc finger transcription factor -

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Basic information

Entry
Database: PDB / ID: 6wlh
TitleRNA complex of WT1 zinc finger transcription factor
Components
  • RNA (29-MER)
  • Wilms tumor protein
KeywordsTRANSCRIPTION / complex / 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
RNA / RNA (> 10) / Wilms tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsWright, P.E. / Dyson, H.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM36643 United States
CitationJournal: Biochemistry / Year: 2020
Title: RNA Binding by the KTS Splice Variants of Wilms' Tumor Suppressor Protein WT1.
Authors: Nishikawa, T. / Wojciak, J.M. / Dyson, H.J. / Wright, P.E.
History
DepositionApr 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wilms tumor protein
B: RNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9786
Polymers23,7162
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3740 Å2
ΔGint-23 kcal/mol
Surface area11780 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 800structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Wilms tumor protein / WT33


Mass: 14417.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / Plasmid: pWT-4-
Details (production host): see Laity et al. Biochemistry 2000
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19544
#2: RNA chain RNA (29-MER)


Mass: 9298.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic23D HNCA
122isotropic23D HN(CA)CB
132isotropic23D HNCO
142isotropic23D (H)CCH-TOCSY
151isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] WT1 zinc finger domain, 10 mM [U-2H] Tris, 40 mM KCl, 10 mM DTT, 5 uM ZnSO4, 2 mM NaN3, 0.5 mM RNA (29-MER), 90% H2O/10% D2O15N sample90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] WT1 zinc finger domain, 0.5 mM RNA (29-MER), 10 mM [U-2H] TRIS, 40 mM potassium chloride, 10 mM DTT, 5 uM ZnSO4, 0.5 mM sodium azide, 90% H2O/10% D2O15N 13C90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMWT1 zinc finger domain[U-15N]1
10 mMTris[U-2H]1
40 mMKClnatural abundance1
10 mMDTTnatural abundance1
5 uMZnSO4natural abundance1
2 mMNaN3natural abundance1
0.5 mMRNA (29-MER)natural abundance1
0.5 mMWT1 zinc finger domain[U-99% 13C; U-99% 15N]2
0.5 mMRNA (29-MER)natural abundance2
10 mMTRIS[U-2H]2
40 mMpotassium chloridenatural abundance2
10 mMDTTnatural abundance2
5 uMZnSO4natural abundance2
0.5 mMsodium azidenatural abundance2
Sample conditionsDetails: See BMRB 50236 for other conditions / Ionic strength: 40 mM KCl mM / Label: 1 / pH: 7.1 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE9001
Bruker DRXBrukerDRX8002cryoprobe
Bruker AVANCEBrukerAVANCE7503
Bruker AVANCEBrukerAVANCE5004
Bruker DRXBrukerDRX6005

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 800 / Conformers submitted total number: 20

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