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- PDB-8c42: Ternary structure of 14-3-3sigma, PKA-responsive ERa phosphopepti... -

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Basic information

Entry
Database: PDB / ID: 8c42
TitleTernary structure of 14-3-3sigma, PKA-responsive ERa phosphopeptide and Fusicoccin-A
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsPEPTIDE BINDING PROTEIN / 14-3-3 / hub-protein / ERa F-domain phosphopeptide
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 / epithelial cell development / keratinocyte development / keratinization / prostate epithelial cord elongation / 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 / : / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / RHO GTPases activate PKNs / protein localization to chromatin / protein kinase A signaling / TBP-class protein binding / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein export from nucleus / negative regulation of innate immune response / 14-3-3 protein binding / 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 / transcription corepressor binding / positive regulation of protein export from nucleus / negative regulation of miRNA transcription / cellular response to estradiol stimulus / stem cell proliferation / 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 / SUMOylation of intracellular receptors / euchromatin / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription coactivator binding / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / Nuclear Receptor transcription pathway / positive regulation of DNA-binding transcription factor activity / response to estrogen / male gonad development / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / 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 / regulation of inflammatory response / fibroblast proliferation / 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
De-acetylated Fusicoccin / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSomsen, B.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)711.017.014 Netherlands
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Molecular basis and dual ligand regulation of tetrameric estrogen receptor alpha /14-3-3 zeta protein complex.
Authors: Somsen, B.A. / Sijbesma, E. / Leysen, S. / Honzejkova, K. / Visser, E.J. / Cossar, P.J. / Obsil, T. / Brunsveld, L. / Ottmann, C.
History
DepositionDec 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[3]

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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)28,1966
Polymers27,4842
Non-polymers7124
Water4,810267
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)56,39112
Polymers54,9684
Non-polymers1,4238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4360 Å2
ΔGint-35 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.726, 111.773, 62.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

MG

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Components

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


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GAMGS at the beginning (-5 to -1) are part of the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Estrogen receptor / / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 940.939 Da / Num. of mol.: 1 / Mutation: F591R; P592R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SIT / De-acetylated Fusicoccin / [(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl] ethanoate


Mass: 638.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H54O11 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.095 M Hepes pH 7.1, 0.19 M CaCl2, 25% PEG400, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→45.41 Å / Num. obs: 54766 / % possible obs: 97.2 % / Redundancy: 13.6 % / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 1.4→1.43 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2615 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
Cootmodel building
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.4→45.41 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 5255 4.99 %
Rwork0.1803 --
obs0.1811 54760 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 48 267 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062026
X-RAY DIFFRACTIONf_angle_d1.0312755
X-RAY DIFFRACTIONf_dihedral_angle_d8.388324
X-RAY DIFFRACTIONf_chiral_restr0.207311
X-RAY DIFFRACTIONf_plane_restr0.008359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.28141530.29573097X-RAY DIFFRACTION90
1.42-1.430.27451860.24923278X-RAY DIFFRACTION95
1.43-1.450.28511790.23273204X-RAY DIFFRACTION94
1.45-1.470.25051260.2153375X-RAY DIFFRACTION96
1.47-1.490.2161660.20253303X-RAY DIFFRACTION96
1.49-1.510.21571690.20183300X-RAY DIFFRACTION97
1.51-1.530.23961740.19323308X-RAY DIFFRACTION96
1.53-1.550.18611690.18693374X-RAY DIFFRACTION97
1.55-1.580.17021670.18653320X-RAY DIFFRACTION97
1.58-1.60.20662070.17963304X-RAY DIFFRACTION96
1.6-1.630.20141580.16873174X-RAY DIFFRACTION93
1.63-1.660.20211640.1733362X-RAY DIFFRACTION97
1.66-1.690.1921560.1673351X-RAY DIFFRACTION97
1.69-1.730.21211700.17273396X-RAY DIFFRACTION98
1.73-1.770.19681910.18223360X-RAY DIFFRACTION98
1.77-1.810.22661880.17533337X-RAY DIFFRACTION98
1.81-1.850.16831700.1883350X-RAY DIFFRACTION98
1.85-1.90.18211840.18123399X-RAY DIFFRACTION98
1.9-1.960.18161880.17243355X-RAY DIFFRACTION98
1.96-2.020.20612120.17583365X-RAY DIFFRACTION98
2.02-2.090.19031970.16563361X-RAY DIFFRACTION99
2.09-2.180.15691670.17033405X-RAY DIFFRACTION98
2.18-2.280.19331600.16943205X-RAY DIFFRACTION93
2.28-2.40.21831720.17483429X-RAY DIFFRACTION99
2.4-2.550.20031660.18263408X-RAY DIFFRACTION99
2.55-2.740.25091980.18823423X-RAY DIFFRACTION99
2.74-3.020.20491690.1923433X-RAY DIFFRACTION100
3.02-3.460.1921860.17943440X-RAY DIFFRACTION99
3.46-4.350.16811730.16393271X-RAY DIFFRACTION96
4.36-45.410.17121900.17943451X-RAY DIFFRACTION100

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