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Yorodumi- PDB-2zr4: Crystal structure of a mutant PIN1 peptidyl-prolyl cis-trans isomerase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zr4 | ||||||
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Title | Crystal structure of a mutant PIN1 peptidyl-prolyl cis-trans isomerase | ||||||
Components | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | ||||||
Keywords | ISOMERASE / PIN1 mutant (S32A) / Cell cycle / Nucleus / Phosphoprotein / Rotamase | ||||||
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 / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / 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 / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / postsynaptic cytosol / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / protein peptidyl-prolyl isomerization / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / : / ciliary basal body / positive regulation of GTPase activity / 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 / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / negative regulation of protein catabolic process / neuron differentiation / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / positive regulation of protein phosphorylation / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Jobichen, C. / Yih-Cherng, L. / Sivaraman, J. | ||||||
Citation | Journal: To be Published Title: Structural studies on PIN1 mutants Authors: Jobichen, C. / Yih-Cherng, L. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zr4.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zr4.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/2zr4 ftp://data.pdbj.org/pub/pdb/validation_reports/zr/2zr4 | HTTPS FTP |
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-Related structure data
Related structure data | 2zqsC 2zqtC 2zquC 2zqvC 2zr5C 2zr6C 1pinS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18255.309 Da / Num. of mol.: 1 / Mutation: S32A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q13526, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-1PG / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.5M ammonium sulfate, 100mM HEPES-NA(pH7.5), 2% PEG400, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2006 |
Radiation | Monochromator: CN1707 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 16318 / Num. obs: 15430 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.062 / Net I/σ(I): 15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PIN Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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