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Yorodumi- PDB-7ort: Ternary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ176 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ort | ||||||
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Title | Ternary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ176 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / protein-peptide complex small-molecule | ||||||
Function / homology | Function and homology information cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / regulation of exit from mitosis ...cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / regulation of exit from mitosis / epithelial cell proliferation involved in prostate gland development / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / ubiquitin ligase activator activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / RHO GTPases activate CIT / nuclear export / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / cellular response to antibiotic / Cul4A-RING E3 ubiquitin ligase complex / molecular function inhibitor activity / negative regulation of kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to lithium ion / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / p53-Dependent G1 DNA Damage Response / protein kinase inhibitor activity / PTK6 Regulates Cell Cycle / regulation of cell-cell adhesion / regulation of G1/S transition of mitotic cell cycle / Constitutive Signaling by AKT1 E17K in Cancer / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of vascular associated smooth muscle cell proliferation / inner ear development / Regulation of localization of FOXO transcription factors / cellular response to organic cyclic compound / keratinocyte proliferation / negative regulation of mitotic cell cycle / phosphoserine residue binding / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / response to amino acid / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to cadmium ion / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to glucose / Cyclin E associated events during G1/S transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of protein localization / RHO GTPases activate PKNs / Notch signaling pathway / positive regulation of microtubule polymerization / protein sequestering activity / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / protein kinase A signaling / FLT3 Signaling / protein export from nucleus / Hsp70 protein binding / negative regulation of innate immune response / regulation of cell migration / positive regulation of cell adhesion / cyclin binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / positive regulation of DNA replication / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / sensory perception of sound / negative regulation of protein kinase activity / placenta development / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / negative regulation of cell growth / SCF(Skp2)-mediated degradation of p27/p21 / response to peptide hormone / positive regulation of protein catabolic process / G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage / Cyclin D associated events in G1 / cellular senescence / protein localization / response to estradiol / regulation of protein localization / heart development / protein-folding chaperone binding / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Centorrino, F. / Wu, Q. / Ottmann, C. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: A crystallography-based study of fragment extensions into the 14-3-3 binding groove Authors: Centorrino, F. / Wu, Q. / Cossar, P. / Brunsveld, L. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ort.cif.gz | 130.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ort.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 7ort.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ort_validation.pdf.gz | 750.4 KB | Display | wwPDB validaton report |
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Full document | 7ort_full_validation.pdf.gz | 750.9 KB | Display | |
Data in XML | 7ort_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 7ort_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/7ort ftp://data.pdbj.org/pub/pdb/validation_reports/or/7ort | HTTPS FTP |
-Related structure data
Related structure data | 7opwC 7oq7C 7oq8C 7oq9C 7oqaC 7oqgC 7oqjC 7oqsC 7oquC 7oqwC 7or3C 7or5C 7or7C 7or8C 7orgC 7orhC 7orsC 4jc3S 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 on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AP
#1: Protein | Mass: 28226.518 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 BL21(DE3) (bacteria) / References: UniProt: P31947 |
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#2: Protein/peptide | Mass: 1522.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P46527 |
-Non-polymers , 4 types, 203 molecules
#3: Chemical | ChemComp-0HP / ~{ | ||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.43 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.095 M Hepes pH7.3, 26%PEG 400, 0.19 M CaCl2, and 5 % Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→41.75 Å / Num. obs: 12594 / % possible obs: 99 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.05 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.33→2.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 17.2 / Num. unique obs: 539 / CC1/2: 0.993 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4jc3 Resolution: 2.33→41.75 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7937 / 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: 16.9 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→41.75 Å
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Refine LS restraints |
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LS refinement shell |
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