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Yorodumi- PDB-6bzd: Structure of 14-3-3 gamma R57E mutant bound to GlcNAcylated peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bzd | ||||||
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Title | Structure of 14-3-3 gamma R57E mutant bound to GlcNAcylated peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / reader protein | ||||||
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 / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / 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 / Activation of BAD and translocation to mitochondria / regulation of signal transduction / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / 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 / 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 / protein sequestering activity / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / protein kinase C binding / insulin-like growth factor receptor binding / negative regulation of protein kinase activity / regulation of synaptic plasticity / 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 / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structural basis of O-GlcNAc recognition by mammalian 14-3-3 proteins. Authors: Toleman, C.A. / Schumacher, M.A. / Yu, S.H. / Zeng, W. / Cox, N.J. / Smith, T.J. / Soderblom, E.J. / Wands, A.M. / Kohler, J.J. / Boyce, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bzd.cif.gz | 202.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bzd.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 6bzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bzd_validation.pdf.gz | 493.6 KB | Display | wwPDB validaton report |
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Full document | 6bzd_full_validation.pdf.gz | 523 KB | Display | |
Data in XML | 6bzd_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 6bzd_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/6bzd ftp://data.pdbj.org/pub/pdb/validation_reports/bz/6bzd | HTTPS FTP |
-Related structure data
Related structure data | 6byjC 6bykC 6bylC 5usk 5usm 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: 28177.311 Da / Num. of mol.: 4 / Mutation: R57E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli (E. coli) / References: UniProt: P61981 #2: Protein/peptide | Mass: 2012.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Sugar | #4: 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: 2.53 Å3/Da / Density % sol: 51.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 25% PEG 4000, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→65.024 Å / Num. obs: 31410 / % possible obs: 95.7 % / Redundancy: 2.5 % / CC1/2: 0.997 / Rsym value: 0.04 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.67→2.8 Å / Mean I/σ(I) obs: 5.8 / CC1/2: 0.997 / Rpim(I) all: 0.486 / Rsym value: 0.648 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5USK 5usk Resolution: 2.67→65.024 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 159.56 Å2 / Biso mean: 72.6 Å2 / Biso min: 27.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.67→65.024 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: 8
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