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Yorodumi- PDB-6a5s: Structure of 14-3-3 gamma in complex with TFEB 14-3-3 binding motif -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a5s | |||||||||
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Title | Structure of 14-3-3 gamma in complex with TFEB 14-3-3 binding motif | |||||||||
Components |
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Keywords | TRANSCRIPTION / PHOSPHOSERIN / REGULATION / TRANSCRIPTION FACTOR | |||||||||
Function / homology | Function and homology information phosphorylation-dependent protein binding / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation ...phosphorylation-dependent protein binding / regulation of neuron differentiation / protein kinase C inhibitor activity / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation / 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 / Recruitment of mitotic centrosome proteins and complexes / negative regulation of TORC1 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / insulin-like growth factor receptor binding / protein sequestering activity / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / protein kinase C binding / negative regulation of protein kinase activity / regulation of synaptic plasticity / cellular response to insulin stimulus / receptor tyrosine kinase binding / Regulation of PLK1 Activity at G2/M Transition / protein localization / presynapse / protein domain specific binding / focal adhesion / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | |||||||||
Authors | Xu, Y. / Ren, J.Q. / Feng, W. | |||||||||
Citation | Journal: Autophagy / Year: 2019 Title: YWHA/14-3-3 proteins recognize phosphorylated TFEB by a noncanonical mode for controlling TFEB cytoplasmic localization. Authors: Xu, Y. / Ren, J. / He, X. / Chen, H. / Wei, T. / Feng, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a5s.cif.gz | 221 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a5s.ent.gz | 175 KB | Display | PDB format |
PDBx/mmJSON format | 6a5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a5s_validation.pdf.gz | 491.8 KB | Display | wwPDB validaton report |
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Full document | 6a5s_full_validation.pdf.gz | 496.6 KB | Display | |
Data in XML | 6a5s_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 6a5s_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/6a5s ftp://data.pdbj.org/pub/pdb/validation_reports/a5/6a5s | HTTPS FTP |
-Related structure data
Related structure data | 6a5qC 3uzdS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28423.668 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P61981 #2: Protein/peptide | Mass: 1557.616 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.77 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 7.3 Details: 0.1 M Tris-HCl, 0.2 M calcium acetate, and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→50 Å / Num. obs: 73457 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.099→2.14 Å / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3618 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UZD Resolution: 2.099→44.044 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.08 Å2 / Biso mean: 25.3333 Å2 / Biso min: 8.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.099→44.044 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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