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Yorodumi- PDB-2ruc: Solution structure of the peptidyl prolyl cis-trans isomerase dom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ruc | ||||||
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Title | Solution structure of the peptidyl prolyl cis-trans isomerase domain of human Pin1 with sulfate ion | ||||||
Components | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | ||||||
Keywords | ISOMERASE / protein/cis-trans-isomerase / PPIase | ||||||
Function / homology | Function and homology information cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein stability / tau protein binding / neuron differentiation / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of GTPase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / protein stabilization / response to hypoxia / nuclear speck / positive regulation of protein phosphorylation / cell cycle / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Xu, N. / Tamari, Y. / Tochio, N. / Tate, S. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: The C113D mutation in human Pin1 causes allosteric structural changes in the phosphate binding pocket of the PPIase domain through the tug of war in the dual-histidine motif. Authors: Xu, N. / Tochio, N. / Wang, J. / Tamari, Y. / Uewaki, J. / Utsunomiya-Tate, N. / Igarashi, K. / Shiraki, T. / Kobayashi, N. / Tate, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ruc.cif.gz | 398.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ruc.ent.gz | 333.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ruc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/2ruc ftp://data.pdbj.org/pub/pdb/validation_reports/ru/2ruc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13121.732 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 51-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.8 mM [U-13C; U-15N] wild type hPin1 PPIase domain-1, 100 mM sodium sulfate-2, 50 mM sodium phosphate-3, 5 mM EDTA-4, 1 mM DTT-5, 0.03 % sodium azide-6, H2O Solvent system: 94.12% H2O, 5.88% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 6.6 / Pressure: ambient / Temperature: 299 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 10 / Representative conformer: 1 |