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- PDB-7oq7: Ternary complex of 14-3-3 sigma, Estrogen Receptor alfa phosphope... -

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Basic information

Entry
Database: PDB / ID: 7oq7
TitleTernary complex of 14-3-3 sigma, Estrogen Receptor alfa phosphopeptide, and WQ162
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsSIGNALING PROTEIN / protein-peptide complex small-molecule
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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of epidermal cell division ...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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of epidermal cell division / epithelial cell proliferation involved in mammary gland duct elongation / protein kinase C inhibitor activity / prostate epithelial cord elongation / positive regulation of epidermal cell differentiation / keratinocyte development / epithelial cell development / keratinization / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / regulation of cell-cell adhesion / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / cAMP/PKA signal transduction / androgen metabolic process / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cellular response to estrogen stimulus / phosphoserine residue binding / mammary gland alveolus development / estrogen response element binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / negative regulation of stem cell proliferation / RNA polymerase II preinitiation complex assembly / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein localization to chromatin / positive regulation of protein localization / 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 / positive regulation of cell adhesion / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / ESR-mediated signaling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / positive regulation of protein export from nucleus / transcription corepressor binding / negative regulation of protein kinase activity / stem cell proliferation / 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 / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / intracellular protein localization / response to estradiol / PIP3 activates AKT signaling / regulation of protein localization / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / regulation of inflammatory response
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 / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. ...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 / 14-3-3 protein sigma / 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
Chem-09W / BETA-MERCAPTOETHANOL / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCentorrino, F. / Ottmann, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission675179European Union
CitationJournal: 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
DepositionJun 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8548
Polymers29,9372
Non-polymers9176
Water4,324240
1
A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules

A: 14-3-3 protein sigma
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,70916
Polymers59,8754
Non-polymers1,83412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4930 Å2
ΔGint-60 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.609, 110.745, 61.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-305-

MG

21A-631-

HOH

31A-635-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 28210.518 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
#2: Protein/peptide Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 1726.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372

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Non-polymers , 5 types, 246 molecules

#3: Chemical ChemComp-09W / ~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-2,3-dihydro-1-benzofuran-7-carboxamide


Mass: 377.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.5, 26%PEG 400, 0.19 M CaCl2, and 5 % Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.6→41.01 Å / Num. obs: 37197 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.01 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.101 / Net I/σ(I): 6.5
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.027 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1811 / CC1/2: 0.487 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.6→41.01 Å / SU ML: 0.2145 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.3843 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1975 3485 5.02 %
Rwork0.1794 65948 -
obs0.1803 37183 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 61 240 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961975
X-RAY DIFFRACTIONf_angle_d1.08832677
X-RAY DIFFRACTIONf_chiral_restr0.0444287
X-RAY DIFFRACTIONf_plane_restr0.0054351
X-RAY DIFFRACTIONf_dihedral_angle_d13.84921201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.32841420.31162634X-RAY DIFFRACTION97.57
1.62-1.650.30911430.30332681X-RAY DIFFRACTION97.75
1.65-1.670.28241410.29572616X-RAY DIFFRACTION98.04
1.67-1.70.35071430.2972670X-RAY DIFFRACTION97.4
1.7-1.720.30711380.29442612X-RAY DIFFRACTION97.28
1.72-1.750.31561400.2852672X-RAY DIFFRACTION97.67
1.75-1.790.29751380.26292627X-RAY DIFFRACTION98.33
1.79-1.820.24791480.24042711X-RAY DIFFRACTION98.28
1.82-1.860.26981360.2442626X-RAY DIFFRACTION97.91
1.86-1.90.24611350.22242667X-RAY DIFFRACTION97.53
1.9-1.940.25291410.2242660X-RAY DIFFRACTION97.97
1.94-1.990.25751400.21472633X-RAY DIFFRACTION97.4
1.99-2.040.26491380.20932649X-RAY DIFFRACTION97.04
2.04-2.10.23951390.192651X-RAY DIFFRACTION97.48
2.1-2.170.18561380.17672596X-RAY DIFFRACTION96.92
2.17-2.250.17221380.1682658X-RAY DIFFRACTION96.68
2.25-2.340.15511360.14992624X-RAY DIFFRACTION96.64
2.34-2.450.19441440.16022600X-RAY DIFFRACTION96.31
2.45-2.570.17971390.15982642X-RAY DIFFRACTION97.34
2.57-2.740.16031340.1622612X-RAY DIFFRACTION96.72
2.74-2.950.15731420.15822616X-RAY DIFFRACTION96.2
2.95-3.240.18751320.15532575X-RAY DIFFRACTION94.82
3.24-3.710.1741350.14522592X-RAY DIFFRACTION95.79
3.71-4.680.15361430.1372622X-RAY DIFFRACTION96.11
4.68-41.010.18251420.17612702X-RAY DIFFRACTION99.58

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