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Yorodumi- PDB-5n10: Cucurbit[8]uril and 14-3-3 based binary bivalent supramolecular-p... -
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-Basic information
Entry | Database: PDB / ID: 5n10 | ||||||||||||
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Title | Cucurbit[8]uril and 14-3-3 based binary bivalent supramolecular-protein assembly platform | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / supramolecular complex / scaffold protein / host-guest | ||||||||||||
Function / homology | Function and homology information negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling ...negative regulation of protein dephosphorylation / cytoplasmic sequestering of protein / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / MTOR signalling / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / Frs2-mediated activation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / positive regulation of catalytic activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / protein kinase inhibitor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / mTORC1-mediated signalling / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / Regulation of localization of FOXO transcription factors / androgen metabolic process / steroid hormone receptor signaling pathway / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / protein targeting / estrogen response element binding / 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 canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / stem cell differentiation / nuclear estrogen receptor binding / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / SUMOylation of intracellular receptors / euchromatin / MAP2K and MAPK activation / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / histone deacetylase binding / Nuclear Receptor transcription pathway / response to estrogen / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / Signaling by BRAF and RAF1 fusions / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / melanosome / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | de Vink, P.J. / Ottmann, C. | ||||||||||||
Funding support | Netherlands, Germany, 3items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3. Authors: de Vink, P.J. / Briels, J.M. / Schrader, T. / Milroy, L.G. / 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 | 5n10.cif.gz | 224.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n10.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 5n10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n10_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5n10_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5n10_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 5n10_validation.cif.gz | 40.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/5n10 ftp://data.pdbj.org/pub/pdb/validation_reports/n1/5n10 | HTTPS FTP |
-Related structure data
Related structure data | 2bq0S S: Starting model for refinement |
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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
-Protein/peptide , 1 types, 3 molecules FCD
#1: Protein/peptide | Mass: 1532.544 Da / Num. of mol.: 3 / Fragment: UNP residues 584-595 / Mutation: T593TPO / Source method: obtained synthetically Details: peptide derived from Estrogen receptor alpha modified with a FGG tag Source: (synth.) Homo sapiens (human) / References: UniProt: P03372 |
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-14-3-3 protein ... , 2 types, 2 molecules AB
#2: Protein | Mass: 28114.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31946 |
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#3: Protein | Mass: 28386.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MTMDKSELVQ KAKLAEQAER YDDMAAAMKA VTEQGHELSN EERNLLSVAY KNVVGARRSS WRVISSIEQK TERNEKKQQM GKEYREKIEA ELQDICNDVL ELLDKYLIPN ATQPESKVFY LKMKGDYFRY LSEVASGDNK QTTVSNSQQA YQEAFEISKK EMQPTHPIRL ...Details: MTMDKSELVQ KAKLAEQAER YDDMAAAMKA VTEQGHELSN EERNLLSVAY KNVVGARRSS WRVISSIEQK TERNEKKQQM GKEYREKIEA ELQDICNDVL ELLDKYLIPN ATQPESKVFY LKMKGDYFRY LSEVASGDNK QTTVSNSQQA YQEAFEISKK EMQPTHPIRL GLALNFSVFY YEILNSPEKA CSLAKTAFDE AIAELDTLNE ESYKDSTLIM QLLRDNLTLW TSENQGDEGD AGEGEN Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31946 |
-Non-polymers , 3 types, 554 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-C8L / |
#6: 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: 2.91 Å3/Da / Density % sol: 57.76 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 1500, sodium citrate / Temp details: coolroom |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97798 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97798 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→66.14 Å / Num. obs: 92397 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rsym value: 0.074 / Net I/σ(I): 13.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BQ0 Resolution: 1.6→50.322 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→50.322 Å
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Refine LS restraints |
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LS refinement shell |
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