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Yorodumi- PDB-6hkf: Ternary complex of Estrogen Receptor alpha peptide and 14-3-3 sig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hkf | ||||||
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Title | Ternary complex of Estrogen Receptor alpha peptide and 14-3-3 sigma C42 mutant bound to disulfide fragment PPI stabilizer 4 | ||||||
Components |
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Keywords | PROTEIN BINDING / protein-protein interaction / fragment / stabilizer / tethering | ||||||
Function / homology | Function and homology information regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / epithelial cell proliferation involved in mammary gland duct elongation / keratinocyte development / keratinization / epithelial cell development / prostate epithelial cord elongation / regulation of cell-cell adhesion / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / Regulation of localization of FOXO transcription factors / steroid hormone receptor signaling pathway / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / mammary gland alveolus development / cellular response to estrogen stimulus / establishment of skin barrier / estrogen response element binding / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / nuclear receptor-mediated steroid hormone signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / positive regulation of protein localization / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / protein localization to chromatin / 14-3-3 protein binding / estrogen receptor signaling pathway / protein sequestering activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein kinase A signaling / steroid binding / TBP-class protein binding / nitric-oxide synthase regulator activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / ESR-mediated signaling / transcription corepressor binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of miRNA transcription / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / positive regulation of nitric-oxide synthase activity / stem cell proliferation / stem cell differentiation / transcription coregulator binding / cellular response to estradiol stimulus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / nuclear estrogen receptor binding / TP53 Regulates Metabolic Genes / positive regulation of DNA-binding transcription factor activity / negative regulation of protein kinase activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / protein localization / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / regulation of protein localization / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / fibroblast proliferation / positive regulation of cell growth Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||
Authors | Sijbesma, E. / Hallenbeck, K.K. / Leysen, S. / Arkin, M.R. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2019 Title: Site-Directed Fragment-Based Screening for the Discovery of Protein-Protein Interaction Stabilizers. Authors: Sijbesma, E. / Hallenbeck, K.K. / Leysen, S. / de Vink, P.J. / Skora, L. / Jahnke, W. / Brunsveld, L. / Arkin, M.R. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hkf.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hkf.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 6hkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hkf_validation.pdf.gz | 863.3 KB | Display | wwPDB validaton report |
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Full document | 6hkf_full_validation.pdf.gz | 863.7 KB | Display | |
Data in XML | 6hkf_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6hkf_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/6hkf ftp://data.pdbj.org/pub/pdb/validation_reports/hk/6hkf | HTTPS FTP |
-Related structure data
Related structure data | 6hhpC 6hkbC 6hmtC 6hmuC 6hn2C 4jc3S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 / Mutation: C38N, N42C 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: 870.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372 | ||||
#3: Chemical | #4: Chemical | ChemComp-G8T / ( | #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: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 0.095M Hepes, 0.19M CaCl2, 5% glycerol, 26% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.46 Å / Num. obs: 26955 / % possible obs: 99.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.18 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.047 / Rsym value: 0.043 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Mean I/σ(I) obs: 8.3 / Num. unique obs: 1428 / CC1/2: 0.973 / Rrim(I) all: 0.198 / Rsym value: 0.176 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JC3 Resolution: 1.801→34.282 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.23 Å2 / Biso mean: 13.1832 Å2 / Biso min: 2.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→34.282 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: 9
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