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

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Basic information

Entry
Database: PDB / ID: 7opw
TitleTernary complex of 14-3-3 sigma, Estrogen Receptor alfa phosphopeptide, and WQ136
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 / regulation of epidermal cell division / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / protein kinase C inhibitor activity ...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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / protein kinase C inhibitor activity / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / prostate epithelial cord elongation / epithelial cell development / 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 / steroid hormone mediated signaling pathway / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / establishment of skin barrier / cellular response to estrogen stimulus / estrogen response element binding / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / positive regulation of phospholipase C activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / protein kinase A signaling / Nuclear signaling by ERBB4 / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / protein export from nucleus / negative regulation of innate immune response / nitric-oxide synthase regulator activity / ESR-mediated signaling / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / 14-3-3 protein binding / transcription corepressor binding / positive regulation of protein export from nucleus / negative regulation of miRNA transcription / stem cell proliferation / cellular response to estradiol stimulus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling
Similarity search - Function
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. ...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 / Zinc finger, C4 type (two domains) / 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
Similarity search - Domain/homology
Chem-0AW / BETA-MERCAPTOETHANOL / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 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)31,2329
Polymers29,9372
Non-polymers1,2957
Water4,864270
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)62,46418
Polymers59,8754
Non-polymers2,58914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4830 Å2
ΔGint-62 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.981, 110.495, 61.228
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-304-

MG

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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, 277 molecules

#3: Chemical ChemComp-0AW / ~{N}-[(5-carbamimidoyl-3-phenyl-thiophen-2-yl)methyl]-2,3-dihydro-1-benzofuran-5-carboxamide


Mass: 377.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H19N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M HEPES pH7.5, 0.19 M CaCl2, 5% glycerol, 26% PEG 400.

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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: 1.81→41.02 Å / Num. obs: 25588 / % possible obs: 99.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.27 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.168 / Net I/σ(I): 4.4
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 1 / Num. unique obs: 1491 / CC1/2: 0.506 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jc3

4jc3


Resolution: 1.81→41.02 Å / SU ML: 0.2473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8418 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2291 2377 4.98 %
Rwork0.1864 45333 -
obs0.1885 25578 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.95 Å2
Refinement stepCycle: LAST / Resolution: 1.81→41.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 88 270 2168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861946
X-RAY DIFFRACTIONf_angle_d1.18562634
X-RAY DIFFRACTIONf_chiral_restr0.0413282
X-RAY DIFFRACTIONf_plane_restr0.0064341
X-RAY DIFFRACTIONf_dihedral_angle_d16.00171167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.850.32151370.30022636X-RAY DIFFRACTION95.92
1.85-1.890.32271410.28762628X-RAY DIFFRACTION97.36
1.89-1.930.33121390.2882665X-RAY DIFFRACTION97.02
1.93-1.980.30871400.27422640X-RAY DIFFRACTION96.03
1.98-2.030.28871350.252651X-RAY DIFFRACTION96.47
2.03-2.090.32131410.22622701X-RAY DIFFRACTION98.07
2.09-2.160.24431430.21322663X-RAY DIFFRACTION98.15
2.16-2.240.26461400.19812697X-RAY DIFFRACTION98.37
2.24-2.330.20481390.17772673X-RAY DIFFRACTION98.29
2.33-2.430.20471430.17012694X-RAY DIFFRACTION98.2
2.43-2.560.27021380.17132684X-RAY DIFFRACTION97.18
2.56-2.720.24741350.17782612X-RAY DIFFRACTION96.52
2.72-2.930.20381410.17182649X-RAY DIFFRACTION96.37
2.93-3.230.19921410.17182668X-RAY DIFFRACTION97.81
3.23-3.690.22261420.15852716X-RAY DIFFRACTION98.42
3.69-4.650.18531410.14292686X-RAY DIFFRACTION98.23
4.65-41.020.19011410.17752670X-RAY DIFFRACTION97.47

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