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Yorodumi- PDB-8adm: Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and sma... -
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-Basic information
Entry | Database: PDB / ID: 8adm | ||||||
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Title | Ternary complex of 14-3-3 sigma, Usp8pS718 phosphopeptide and small molecule stabilizer | ||||||
Components |
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Keywords | SIGNALING PROTEIN / 14-3-3 sigma / Usp8 / small molecule stabilizer | ||||||
Function / homology | Function and homology information regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / protein K48-linked deubiquitination / endosome organization / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / extrinsic component of plasma membrane / regulation of epidermal cell division ...regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / protein K48-linked deubiquitination / endosome organization / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / extrinsic component of plasma membrane / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / protein deubiquitination / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / mitotic cytokinesis / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / 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 / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein kinase A signaling / Regulation of FZD by ubiquitination / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / Downregulation of ERBB2:ERBB3 signaling / cellular response to dexamethasone stimulus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / cellular response to nerve growth factor stimulus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of protein stability / Negative regulation of MET activity / SH3 domain binding / regulation of protein localization / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical Wnt signaling pathway / midbody / positive regulation of cell growth / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ras protein signal transduction / dendritic spine / postsynaptic density / early endosome / endosome membrane / regulation of cell cycle / Ub-specific processing proteases / cadherin binding / cysteine-type endopeptidase activity / glutamatergic synapse / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / proteolysis / extracellular space / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Centorrino, F. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Acs Cent.Sci. / Year: 2023 Title: A Systematic Approach to the Discovery of Protein-Protein Interaction Stabilizers. Authors: Kenanova, D.N. / Visser, E.J. / Virta, J.M. / Sijbesma, E. / Centorrino, F. / Vickery, H.R. / Zhong, M. / Neitz, R.J. / Brunsveld, L. / Ottmann, C. / Arkin, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8adm.cif.gz | 130.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8adm.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 8adm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8adm_validation.pdf.gz | 760.8 KB | Display | wwPDB validaton report |
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Full document | 8adm_full_validation.pdf.gz | 762.5 KB | Display | |
Data in XML | 8adm_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 8adm_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/8adm ftp://data.pdbj.org/pub/pdb/validation_reports/ad/8adm | HTTPS FTP |
-Related structure data
Related structure data | 8a62C 8a65C 8a68C 8a6fC 8a6hC 8afnC 8av0C 1ywtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 1004.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40818, ubiquitinyl hydrolase 1 |
#3: Chemical | ChemComp-O6C / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.67 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer ...Details: 0.1M carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1M buffer system 1 (Imidazole; MES monohydrate) pH 6.5 and 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.84 Å / Num. obs: 34318 / % possible obs: 99.4 % / Redundancy: 13.2 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1669 / CC1/2: 0.832 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YWT Resolution: 1.7→39.84 Å / SU ML: 0.1795 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9639 / Stereochemistry target values: GeoStd + Monomer Library
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→39.84 Å
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Refine LS restraints |
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LS refinement shell |
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