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

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Basic information

Entry
Database: PDB / ID: 4jdd
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


steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / Developmental Lineage of Mammary Gland Alveolar Cells / regulation of cell-cell adhesion / TFIIB-class transcription factor binding ...steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / positive regulation of epidermal cell differentiation / regulation of epidermal cell division / protein kinase C inhibitor activity / Developmental Lineage of Mammary Gland Alveolar Cells / regulation of cell-cell adhesion / TFIIB-class transcription factor binding / negative regulation of smooth muscle cell apoptotic process / establishment of skin barrier / Regulation of localization of FOXO transcription factors / nuclear receptor-mediated steroid hormone signaling pathway / Regulation of GBP-mediated host defense / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Mitochondrial unfolded protein response (UPRmt) / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cAMP/PKA signal transduction / Nuclear signaling by ERBB4 / protein export from nucleus / estrogen receptor signaling pathway / RNA polymerase II preinitiation complex assembly / release of cytochrome c from mitochondria / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of protein kinase activity / RHO GTPases activate PKNs / positive regulation of nitric-oxide synthase activity / steroid binding / positive regulation of protein localization / positive regulation of protein export from nucleus / stem cell differentiation / protein localization to chromatin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 14-3-3 protein binding / ESR-mediated signaling / positive regulation of cell adhesion / negative regulation of miRNA transcription / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of innate immune response / TBP-class protein binding / nuclear estrogen receptor binding / nitric-oxide synthase regulator activity / transcription corepressor binding / negative regulation of canonical NF-kappaB signal transduction / transcription coregulator binding / cellular response to estradiol stimulus / TP53 Regulates Metabolic Genes / SUMOylation of intracellular receptors / intrinsic apoptotic signaling pathway in response to DNA damage / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein sequestering activity / euchromatin / Nuclear Receptor transcription pathway / response to estrogen / beta-catenin binding / nuclear receptor activity / transcription coactivator binding / intracellular protein localization / positive regulation of nitric oxide biosynthetic process / Constitutive Signaling by Aberrant PI3K in Cancer / sequence-specific double-stranded DNA binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / regulation of protein localization / positive regulation of cell growth / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cadherin binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / Golgi apparatus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 14-3-3 protein sigma / Estrogen receptor/oestrogen-related receptor / 14-3-3 proteins signature 2. ...14-3-3 domain / Delta-Endotoxin; domain 1 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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
FUSICOCCIN / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _struct_conn.pdbx_leaving_atom_flag / _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)28,3823
Polymers27,7012
Non-polymers6811
Water1,820101
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)56,7646
Polymers55,4024
Non-polymers1,3622
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3990 Å2
ΔGint-25 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.490, 111.430, 62.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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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-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
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: 2.1→19.8 Å / Num. all: 17090 / Num. obs: 17090 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.566 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 17.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.150.4764.7789621144100
2.15-2.20.3955.6881111034100
2.2-2.30.3266.96145611837100
2.3-2.50.2688.31226562846100
2.5-2.80.1911.36232202899100
2.8-30.13115.94107521340100
3-40.06828.42273123413100
4-60.04737.7614035178899.9
6-80.04638.59351546199.8
8-100.02559.711208163100
10-120.02363.652076100
120.02557.795728974.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.8 Å
Translation2.5 Å19.8 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.8 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.1977 / WRfactor Rwork: 0.1636 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8459 / SU B: 4.347 / SU ML: 0.119 / SU R Cruickshank DPI: 0.2073 / SU Rfree: 0.1758 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 855 5 %RANDOM
Rwork0.1924 ---
obs0.1944 17076 99.82 %-
all-17090 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.51 Å2 / Biso mean: 20.0007 Å2 / Biso min: 0.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.37 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 48 101 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021968
X-RAY DIFFRACTIONr_angle_refined_deg1.9922.0212661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06724.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06315358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5381513
X-RAY DIFFRACTIONr_chiral_restr0.1290.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211452
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.191 54 -
Rwork0.178 1075 -
all-1129 -
obs--100 %

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