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- PDB-4jc3: 14-3-3 protein interaction with Estrogen Receptor Alpha provides ... -

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Basic information

Entry
Database: PDB / ID: 4jc3
Title14-3-3 protein interaction with Estrogen Receptor Alpha provides a novel drug target interface
Components
  • 14-3-3 protein sigma
  • Estrogen receptor Peptide
KeywordsSIGNALING PROTEIN/Peptide / 14-3-3 / ADAPTER PROTEIN / PROTEIN-PROTEIN INTERACTION / SIGNALING PROTEIN-Peptide complex
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
Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBier, D. / Ottmann, C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: Interaction of 14-3-3 proteins with the estrogen receptor alpha F domain provides a drug target interface.
Authors: De Vries-van Leeuwen, I.J. / da Costa Pereira, D. / Flach, K.D. / Piersma, S.R. / Haase, C. / Bier, D. / Yalcin, Z. / Michalides, R. / Feenstra, K.A. / Jimenez, C.R. / de Greef, T.F. / ...Authors: De Vries-van Leeuwen, I.J. / da Costa Pereira, D. / Flach, K.D. / Piersma, S.R. / Haase, C. / Bier, D. / Yalcin, Z. / Michalides, R. / Feenstra, K.A. / Jimenez, C.R. / de Greef, T.F. / Brunsveld, L. / Ottmann, C. / Zwart, W. / de Boer, A.H.
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7745
Polymers27,7012
Non-polymers733
Water3,081171
1
A: 14-3-3 protein sigma
B: Estrogen receptor Peptide
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)55,54810
Polymers55,4024
Non-polymers1466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4240 Å2
ΔGint-43 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.210, 112.490, 62.450
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-302-

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 / Fragment: UNP residues 1-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, NM_006142, SFN / Plasmid: PPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P31947
#2: Protein/peptide Estrogen receptor Peptide


Mass: 1158.109 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 585-595 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.095M HEPES Na, 0.19M calcium chloride, 5% glycerol, 26.6% PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→19.52 Å / Num. all: 18518 / Num. obs: 18505 / % possible obs: 99.78 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.403 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 24.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.05-2.10.3246.85199.3
2.1-2.150.2359.051100
2.15-2.20.20610.311100
2.2-2.30.16712.51100
2.3-2.50.1414.71100
2.5-2.80.10718.881100
2.8-30.0824.251100
3-40.04738.851100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.52 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.471 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23512 926 5 %RANDOM
Rwork0.17787 ---
obs0.18068 17579 99.78 %-
all-18505 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.867 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 3 171 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191921
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9832589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93524.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9191513
X-RAY DIFFRACTIONr_chiral_restr0.1150.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211433
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 59 -
Rwork0.187 1166 -
obs--99.27 %

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