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Yorodumi- PDB-4e2e: Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-mono... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e2e | ||||||
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Title | Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide (YWHAG) from Homo sapiens at 2.25 A resolution | ||||||
Components | 14-3-3 protein gamma | ||||||
Keywords | SIGNALING PROTEIN / 14-3-3 domain / signal transduction / cell signaling / protein binding / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / Partnership for T-Cell Biology / TCELL | ||||||
Function / homology | Function and homology information regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / regulation of signal transduction / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / regulation of signal transduction / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / negative regulation of TORC1 signaling / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / insulin-like growth factor receptor binding / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein sequestering activity / protein kinase C binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / regulation of synaptic plasticity / negative regulation of protein kinase activity / receptor tyrosine kinase binding / cellular response to insulin stimulus / Regulation of PLK1 Activity at G2/M Transition / presynapse / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
Citation | Journal: To be published Title: Crystal structure of a tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activa tion protein, gamma polypeptide (YWHAG) from Homo sapiens at 2.25 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e2e.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e2e.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 4e2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/4e2e ftp://data.pdbj.org/pub/pdb/validation_reports/e2/4e2e | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | CRYSTAL PACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A DIMER AND TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATES IN SOLUTION. |
-Components
#1: Protein | Mass: 28721.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BC020963, YWHAG / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: P61981 |
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#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Sequence details | THIS CONSTRUCT (RESIDUES 1-247) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 1-247) WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.00M LiCl, 20.00% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9786 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→27.685 Å / Num. obs: 14183 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.08 % / Biso Wilson estimate: 52.21 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.83 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→27.685 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9299 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE REFINEMENT WAS RESTRAINED AGAINST THE SAD PHASES 4.1,2-ETHANE DIOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE.
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Displacement parameters | Biso max: 157.11 Å2 / Biso mean: 61.2447 Å2 / Biso min: 23.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→27.685 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.43 Å / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: 21.6854 Å / Origin y: 59.4929 Å / Origin z: 165.915 Å
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