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- PDB-6tl3: Crystal structure of an Estrogen Receptor alpha 8-mer phosphopept... -

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Basic information

Entry
Database: PDB / ID: 6tl3
TitleCrystal structure of an Estrogen Receptor alpha 8-mer phosphopeptide in complex with 14-3-3sigma stabilized by a Pyrrolidone1 derivative
Components
  • 14-3-3 protein sigma
  • Estrogen receptor
KeywordsSIGNALING PROTEIN / Estrogen receptor / 14-3-3 / PPI / stabiliser / 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
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 / 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
Similarity search - Domain/homology
Chem-NJW / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.455 Å
AuthorsAndrei, S.A. / Bosica, F. / Ottmann, C. / O'Mahony, G.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Commission Netherlands
CitationJournal: Chemistry / Year: 2020
Title: Design of Drug-Like Protein-Protein Interaction Stabilizers Guided By Chelation-Controlled Bioactive Conformation Stabilization.
Authors: Bosica, F. / Andrei, S.A. / Neves, J.F. / Brandt, P. / Gunnarsson, A. / Landrieu, I. / Ottmann, C. / O'Mahony, G.
History
DepositionNov 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)27,9153
Polymers27,4562
Non-polymers4591
Water3,315184
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)55,8306
Polymers54,9124
Non-polymers9192
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area3830 Å2
ΔGint-27 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.694, 152.232, 76.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-569-

HOH

31A-575-

HOH

41A-578-

HOH

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Components

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


Mass: 26558.914 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 (E. coli) / References: UniProt: P31947
#2: Protein/peptide Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 896.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372
#3: Chemical ChemComp-NJW / 5-[(2~{S},3~{R})-3-[(~{R})-azanyl(phenyl)methyl]-2-(4-nitrophenyl)-4,5-bis(oxidanylidene)pyrrolidin-1-yl]-2-oxidanyl-benzoic acid


Mass: 459.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H17N3O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris, pH 7.0, 10 % v/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.45→24.111 Å / Num. obs: 13893 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.078 / Rrim(I) all: 0.198 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.516.60.64765309920.8630.2720.7032.2100
10.96-24.045.30.0478831680.9990.0230.05316.890.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.94 Å24.11 Å

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX3500refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jc3

4jc3


Resolution: 2.455→24.111 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.96
RfactorNum. reflection% reflection
Rfree0.2592 679 4.89 %
Rwork0.2097 --
obs0.2121 13882 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.71 Å2 / Biso mean: 39.6118 Å2 / Biso min: 1.52 Å2
Refinement stepCycle: final / Resolution: 2.455→24.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 49 194 2080
Biso mean--35.86 40.69 -
Num. residues----233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4554-2.64480.36251440.2729257299
2.6448-2.91050.2771400.23622606100
2.9105-3.33080.27611320.22782623100
3.3308-4.19280.25741190.1939264299
4.1928-24.1110.20941440.18222760100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.52690.83050.77272.2721-2.81453.8629-0.11510.10880.04980.10630.0050.1141-0.22550.17380.07510.3478-0.06140.03530.1799-0.05910.19539.842529.383724.063
23.55250.0797-3.95341.09580.5665.6848-0.31130.3158-0.3758-0.0011-0.02090.04910.119-0.40090.34040.2573-0.0264-0.02910.2199-0.0370.222420.463225.530732.3949
32.5038-1.848-2.27882.9965-0.94196.60510.03421.37861.0615-1.52130.2293-0.4979-0.2230.76130.33320.9562-0.0259-0.18420.59270.060.01129.466331.19549.0545
42.39291.014-1.67113.08551.15176.60050.14930.51730.0805-0.3972-0.28510.3403-0.3188-1.17530.11840.30730.0435-0.05430.4159-0.04280.243717.96523.850415.3442
50.615-1.21480.35563.46220.48923.01740.06030.0532-0.30530.1482-0.30090.34060.465-0.74230.19370.3619-0.2049-0.00250.4236-0.10320.308719.76538.235514.6146
62.84934.9063-2.79918.5529-5.56488.59310.3673-1.2572-0.46020.8006-0.21090.1776-1.00840.1315-0.0850.3878-0.0797-0.07550.5673-0.03020.441419.713613.256725.436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 37 )A-4 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 105 )A38 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 113 )A106 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 161 )A114 - 161
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 231 )A162 - 231
6X-RAY DIFFRACTION6chain 'B' and (resid 591 through 595 )B591 - 595

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