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- PDB-1m9o: NMR structure of the first Zinc Binding domain of Nup475/TTP/TIS11 -

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Basic information

Entry
Database: PDB / ID: 1m9o
TitleNMR structure of the first Zinc Binding domain of Nup475/TTP/TIS11
ComponentsTristetraproline
KeywordsMETAL BINDING PROTEIN / Cys3His type zinc finger
Function / homology
Function and homology information


regulation of keratinocyte apoptotic process / negative regulation of polynucleotide adenylyltransferase activity / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / positive regulation of intracellular mRNA localization / negative regulation of hematopoietic stem cell differentiation / negative regulation of erythrocyte differentiation / positive regulation of miRNA-mediated gene silencing / RNA destabilization ...regulation of keratinocyte apoptotic process / negative regulation of polynucleotide adenylyltransferase activity / nuclear-transcribed mRNA catabolic process, deadenylation-independent decay / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / positive regulation of deadenylation-independent decapping of nuclear-transcribed mRNA / positive regulation of intracellular mRNA localization / negative regulation of hematopoietic stem cell differentiation / negative regulation of erythrocyte differentiation / positive regulation of miRNA-mediated gene silencing / RNA destabilization / regulation of keratinocyte proliferation / regulation of keratinocyte differentiation / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of myeloid cell differentiation / 3'-UTR-mediated mRNA destabilization / negative regulation of viral transcription / miRNA-mediated gene silencing by inhibition of translation / regulation of tumor necrosis factor production / myeloid cell differentiation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / mRNA 3'-UTR AU-rich region binding / RNA polymerase binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 3'-UTR-mediated mRNA stabilization / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / cellular response to glucocorticoid stimulus / negative regulation of interleukin-2 production / response to starvation / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / p38MAPK cascade / mRNA catabolic process / hematopoietic stem cell differentiation / mRNA transport / positive regulation of fat cell differentiation / cellular response to fibroblast growth factor stimulus / 14-3-3 protein binding / regulation of mRNA stability / cellular response to epidermal growth factor stimulus / P-body / response to wounding / negative regulation of inflammatory response / cytoplasmic stress granule / cellular response to tumor necrosis factor / MAPK cascade / cellular response to lipopolysaccharide / intracellular signal transduction / ribonucleoprotein complex / mRNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Zinc finger, CCCH-type / RNA-binding protein ZFP36-like / CCCH zinc finger / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
mRNA decay activator protein ZFP36
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / CNS, dynamical annealing protocal with molecular dynamic scheme of torsion,torsion,cartesian. Initially only distance restraints from the three Cys to the zinc were restrained. Eventually the His was also restrained, angle restraints added to make the site tetrahedral.
AuthorsAmann, B.T. / Worthington, M.T. / Berg, J.M.
CitationJournal: Biochemistry / Year: 2003
Title: A Cys3His Zinc-Binding Domain from Nup475/Tristetraproline: a Novel Fold with a Disklike Structure
Authors: Amann, B.T. / Worthington, M.T. / Berg, J.M.
History
DepositionJul 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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: Tristetraproline
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0382
Polymers8,9721
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 30structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Tristetraproline / TTP / TIS11A protein / TIS11 / ZFP-36 / Growth factor-inducible nuclear protein NUP475 / TPA ...TTP / TIS11A protein / TIS11 / ZFP-36 / Growth factor-inducible nuclear protein NUP475 / TPA induced sequence 11


Mass: 8972.193 Da / Num. of mol.: 1 / Fragment: zinc binding domain (Residues 91-163) / Mutation: Y143K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nup475 / Plasmid: pET28b, pMW55 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P22893
#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
1112D NOESY
1212D TOCSY
131DQF-COSY
1413D 13C-separated NOESY
1513D 15N-separated NOESY
161HN(CA)CB
17115N-HSQC-TOCSY
18113C-(H)CCH-TOCSY
191HSQCJ WEX

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Sample preparation

DetailsContents: 1.7mM Nup475 with 2.2 Equivalent ZnCl2, 50mM d-Tris pH 5
Solvent system: 90% H20, 10% D20 and 100% D20
Sample conditionsIonic strength: no salt added / pH: 5.8 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98Biosym/Molecular Simulationprocessing
CNS1Brungerstructure solution
VNMR6.1bVariancollection
CNS1Brungerrefinement
RefinementMethod: CNS, dynamical annealing protocal with molecular dynamic scheme of torsion,torsion,cartesian. Initially only distance restraints from the three Cys to the zinc were restrained. Eventually the ...Method: CNS, dynamical annealing protocal with molecular dynamic scheme of torsion,torsion,cartesian. Initially only distance restraints from the three Cys to the zinc were restrained. Eventually the His was also restrained, angle restraints added to make the site tetrahedral.
Software ordinal: 1
Details: 442 NOE restraints, 15 Torsional angle restraints. 15 zinc site restraints, 64 Carbon chemical shifts, and 174 proton chemical restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 23

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