+Open data
-Basic information
Entry | Database: PDB / ID: 3uzd | ||||||
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Title | Crystal structure of 14-3-3 GAMMA | ||||||
Components |
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Keywords | PROTEIN BINDING/HYDROLASE / Structural Genomics / SGC / Structural Genomics Consortium / Mainly Alpha / phosphoserine / phosphothreonine / PROTEIN BINDING-HYDROLASE complex | ||||||
Function / homology | Function and homology information RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase ...RUNX2 regulates chondrocyte maturation / response to denervation involved in regulation of muscle adaptation / negative regulation of myotube differentiation / peptidyl-lysine deacetylation / positive regulation of protein sumoylation / negative regulation of transcription by competitive promoter binding / regulation of protein binding / protein deacetylation / cardiac muscle hypertrophy in response to stress / histone deacetylase / phosphoserine residue binding / protein lysine deacetylase activity / negative regulation of glycolytic process / SUMO transferase activity / histone deacetylase activity / negative regulation of gene expression, epigenetic / regulation of neuron differentiation / B cell activation / type I interferon-mediated signaling pathway / protein kinase C inhibitor activity / Notch-HLH transcription pathway / potassium ion binding / protein sumoylation / RUNX3 regulates p14-ARF / histone deacetylase complex / Regulation of localization of FOXO transcription factors / protein sequestering activity / 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 / transcription repressor complex / SUMOylation of chromatin organization proteins / response to interleukin-1 / AURKA Activation by TPX2 / B cell differentiation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein kinase C binding / TP53 Regulates Metabolic Genes / regulation of synaptic plasticity / negative regulation of protein kinase activity / SUMOylation of intracellular receptors / NOTCH1 Intracellular Domain Regulates Transcription / negative regulation of DNA-binding transcription factor activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / receptor tyrosine kinase binding / histone deacetylase binding / cellular response to insulin stimulus / positive regulation of DNA-binding transcription factor activity / Regulation of PLK1 Activity at G2/M Transition / presynapse / nervous system development / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / molecular adaptor activity / nuclear speck / chromatin remodeling / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / focal adhesion / chromatin / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / membrane / nucleus / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å | ||||||
Authors | Xu, C. / Bian, C. / MacKenzie, F. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Sci.Signal. / Year: 2012 Title: Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock. Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / ...Authors: Xu, C. / Jin, J. / Bian, C. / Lam, R. / Tian, R. / Weist, R. / You, L. / Nie, J. / Bochkarev, A. / Tempel, W. / Tan, C.S. / Wasney, G.A. / Vedadi, M. / Gish, G.D. / Arrowsmith, C.H. / Pawson, T. / Yang, X.J. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uzd.cif.gz | 111.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uzd.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 3uzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/3uzd ftp://data.pdbj.org/pub/pdb/validation_reports/uz/3uzd | HTTPS FTP |
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-Related structure data
Related structure data | 3so8C 3uxgC 3v2oC 3v2xC 3v30C 3v31C 2b05S 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28423.668 Da / Num. of mol.: 1 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 | ||||
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#2: Protein/peptide | Mass: 1876.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: polypeptide(L) / Source: (synth.) Homo sapiens (human) / References: UniProt: P56524, histone deacetylase | ||||
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: 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: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.3M Mg (OAc)2, 20% PEG3350, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→66.48 Å / Num. obs: 24650 / % possible obs: 98.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2B05 Resolution: 1.86→66.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.113 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→66.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.91 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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