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- 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
TitleCucurbit[8]uril and 14-3-3 based binary bivalent supramolecular-protein assembly platform
Components
  • (14-3-3 protein ...) x 2
  • Estrogen receptor
KeywordsTRANSCRIPTION / supramolecular complex / scaffold protein / host-guest
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 / negative regulation of G protein-coupled receptor signaling pathway / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / negative regulation of protein import into nucleus / protein phosphatase inhibitor activity / regulation of toll-like receptor signaling pathway / Frs2-mediated activation / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / protein kinase inhibitor activity / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / mTORC1-mediated signalling / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / Regulation of localization of FOXO transcription factors / cellular response to estrogen stimulus / phosphoserine residue binding / mammary gland alveolus development / estrogen response element binding / Activation of BAD and translocation to mitochondria / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / protein sequestering activity / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / phosphoprotein binding / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / RAF activation / Signaling by high-kinase activity BRAF mutants / transcription coactivator binding / euchromatin / MAP2K and MAPK activation / beta-catenin binding / Nuclear Receptor transcription pathway / histone deacetylase binding / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / Signaling by BRAF and RAF1 fusions / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / intracellular protein localization / melanosome / response to estradiol / PIP3 activates AKT signaling
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...14-3-3 domain / Delta-Endotoxin; domain 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cucurbit[8]uril / Estrogen receptor / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Authorsde Vink, P.J. / Ottmann, C.
Funding support Netherlands, Germany, 3items
OrganizationGrant numberCountry
Netherlands Organization for Scientific Research024.001.035 Netherlands
Netherlands Organization for Scientific Research016.150.366 Netherlands
German Research FoundationCRC1093 Germany
CitationJournal: 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
DepositionFeb 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 2.0Aug 2, 2017Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Estrogen receptor
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5207
Polymers61,0995
Non-polymers1,4212
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-36 kcal/mol
Surface area24990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.807, 57.571, 93.450
Angle α, β, γ (deg.)90.00, 98.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 1 types, 3 molecules FCD

#1: Protein/peptide Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


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 14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


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
#3: Protein 14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


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

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Non-polymers , 3 types, 554 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-C8L / Cucurbit[8]uril


Mass: 1329.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H48N32O16
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG 1500, sodium citrate / Temp details: coolroom

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97798 Å / Relative weight: 1
ReflectionResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BQ0

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
RfactorNum. reflection% reflection
Rfree0.1935 1922 2.08 %
Rwork0.1696 --
obs0.1701 92384 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→50.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 102 552 4584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114480
X-RAY DIFFRACTIONf_angle_d1.1826142
X-RAY DIFFRACTIONf_dihedral_angle_d13.6161819
X-RAY DIFFRACTIONf_chiral_restr0.048654
X-RAY DIFFRACTIONf_plane_restr0.011873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.32721410.2846372X-RAY DIFFRACTION99
1.64-1.68440.27481340.26286419X-RAY DIFFRACTION99
1.6844-1.73390.29081210.246411X-RAY DIFFRACTION99
1.7339-1.78990.26311470.22926361X-RAY DIFFRACTION99
1.7899-1.85390.23341530.20896437X-RAY DIFFRACTION99
1.8539-1.92810.24211270.19836417X-RAY DIFFRACTION99
1.9281-2.01590.22771550.18096412X-RAY DIFFRACTION100
2.0159-2.12210.18481340.16936480X-RAY DIFFRACTION100
2.1221-2.25510.17441310.16076429X-RAY DIFFRACTION100
2.2551-2.42920.19191340.15956520X-RAY DIFFRACTION100
2.4292-2.67370.1971260.16396500X-RAY DIFFRACTION100
2.6737-3.06050.19151320.16866518X-RAY DIFFRACTION100
3.0605-3.85570.18811360.166531X-RAY DIFFRACTION100
3.8557-50.34660.16251510.15116655X-RAY DIFFRACTION100

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