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Yorodumi- PDB-4n84: Crystal structure of 14-3-3zeta in complex with a 12-carbon-linke... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n84 | ||||||
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Title | Crystal structure of 14-3-3zeta in complex with a 12-carbon-linker cyclic peptide derived from ExoS | ||||||
Components |
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Keywords | SIGNALING PROTEIN / 14-3-3 / adaptor protein / protein-protein interaction / cross-link | ||||||
Function / homology | Function and homology information Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / glycosyltransferase activity / Regulation of localization of FOXO transcription factors ...Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / glycosyltransferase activity / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / 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 / negative regulation of TORC1 signaling / negative regulation of innate immune response / nucleotidyltransferase activity / GTPase activator activity / regulation of ERK1 and ERK2 cascade / protein sequestering activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / melanosome / toxin activity / DNA-binding transcription factor binding / blood microparticle / vesicle / transmembrane transporter binding / cadherin binding / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Bier, D. / Glas, A. / Hahne, G. / Grossmann, T. / Ottmann, C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Constrained peptides with target-adapted cross-links as inhibitors of a pathogenic protein-protein interaction. Authors: Glas, A. / Bier, D. / Hahne, G. / Rademacher, C. / Ottmann, C. / Grossmann, T.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n84.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n84.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 4n84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/4n84 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/4n84 | HTTPS FTP |
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-Related 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: 26260.656 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NP_001129171.1, YWHAZ / Plasmid: pProEx HTb / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P63104 #2: Protein/peptide | Mass: 1113.347 Da / Num. of mol.: 2 / Fragment: modified peptide (UNP residues 421-430) / Mutation: L422(MKD),A425(MKD) / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q93SQ3 #3: 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: 4.55 Å3/Da / Density % sol: 72.96 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / pH: 8 Details: 1 M potassium sodium tartrate, 0.1 M sodium chloride, 0.1 M imidazole, pH 8.0, cryoprotectant: 20% glycerol, VAPOR DIFFUSION, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→47.74 Å / Num. all: 35305 / Num. obs: 35246 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.858 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.08 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2488 / WRfactor Rwork: 0.2046 / Occupancy max: 1 / Occupancy min: 0.8 / FOM work R set: 0.8212 / SU B: 6.583 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2333 / SU Rfree: 0.2128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.7 Å2 / Biso mean: 54.4754 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→47.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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