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- PDB-1m9o: NMR structure of the first Zinc Binding domain of Nup475/TTP/TIS11 -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m9o | ||||||
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Title | NMR structure of the first Zinc Binding domain of Nup475/TTP/TIS11 | ||||||
![]() | Tristetraproline | ||||||
![]() | METAL BINDING PROTEIN / Cys3His type zinc finger | ||||||
Function / homology | ![]() 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 erythrocyte differentiation / RNA destabilization / positive regulation of miRNA-mediated gene silencing / regulation of keratinocyte proliferation ...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 erythrocyte differentiation / RNA destabilization / positive regulation of miRNA-mediated gene silencing / regulation of keratinocyte proliferation / regulation of keratinocyte differentiation / positive regulation of mRNA catabolic process / negative regulation of myeloid cell differentiation / nuclear-transcribed mRNA poly(A) tail shortening / multicellular organism development / 3'-UTR-mediated mRNA destabilization / negative regulation of viral transcription / mRNA 3'-UTR AU-rich region binding / miRNA-mediated gene silencing by inhibition of translation / C-C chemokine binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of tumor necrosis factor production / cellular response to fibroblast growth factor stimulus / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / cellular response to glucocorticoid stimulus / RNA polymerase binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / negative regulation of interleukin-2 production / 3'-UTR-mediated mRNA stabilization / p38MAPK cascade / response to starvation / mRNA catabolic process / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of fat cell differentiation / mRNA transport / cellular response to epidermal growth factor stimulus / 14-3-3 protein binding / heat shock protein binding / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / negative regulation of inflammatory response / cytoplasmic stress granule / response to wounding / MAPK cascade / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / intracellular signal transduction / ribonucleoprotein complex / mRNA binding / regulation of transcription by RNA polymerase II / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION 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. | ||||||
![]() | Amann, B.T. / Worthington, M.T. / Berg, J.M. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 293.8 KB | Display | ![]() |
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PDB format | ![]() | 237.2 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 350.3 KB | Display | ![]() |
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Full document | ![]() | 529.9 KB | Display | |
Data in XML | ![]() | 24.4 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 1.7mM Nup475 with 2.2 Equivalent ZnCl2, 50mM d-Tris pH 5 Solvent system: 90% H20, 10% D20 and 100% D20 |
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Sample conditions | Ionic strength: no salt added / pH: 5.8 / Pressure: ambient / Temperature: 293 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz |
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Processing
NMR software |
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Refinement | 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 ...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 representative | Selection criteria: closest to the average | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 23 |