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

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Basic information

Entry
Database: PDB / ID: 6tjm
TitleCrystal structure of an Estrogen Receptor alpha 8-mer phosphopeptide in complex with 14-3-3sigma stabilized by Pyrrolidone1
Components
  • 14-3-3 protein sigma
  • C-terminal phosphopeptide of human estrogen receptor alpha
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 / regulation of epidermal cell division / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...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 / protein kinase C inhibitor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / 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 / TFIIB-class transcription factor binding / androgen metabolic process / 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 / establishment of skin barrier / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / Nuclear signaling by ERBB4 / 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 / 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 / protein export from nucleus / steroid binding / 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 / positive regulation of protein export from nucleus / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / stem cell proliferation / cellular response to estradiol stimulus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / 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 / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / 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-NE5 / Estrogen receptor / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 26, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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: C-terminal phosphopeptide of human estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9244
Polymers27,4402
Non-polymers4852
Water2,288127
1
A: 14-3-3 protein sigma
B: C-terminal phosphopeptide of human estrogen receptor alpha
hetero molecules

A: 14-3-3 protein sigma
B: C-terminal phosphopeptide of human estrogen receptor alpha
hetero molecules

A: 14-3-3 protein sigma
B: C-terminal phosphopeptide of human estrogen receptor alpha
hetero molecules

A: 14-3-3 protein sigma
B: C-terminal phosphopeptide of human estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69816
Polymers109,7598
Non-polymers1,9398
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area10230 Å2
ΔGint-102 kcal/mol
Surface area41920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.841, 152.310, 76.792
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-514-

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
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 C-terminal phosphopeptide of human estrogen receptor alpha


Mass: 896.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NE5 / 5-[(2~{R})-2-(4-nitrophenyl)-4-oxidanyl-5-oxidanylidene-3-(phenylcarbonyl)-2~{H}-pyrrol-1-yl]-2-oxidanyl-benzoic acid


Mass: 460.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H16N2O8 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→76.78 Å / Num. obs: 31900 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.013 / Rrim(I) all: 0.045 / Net I/σ(I): 24 / Num. measured all: 398455 / Scaling rejects: 607
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
1.85-1.911.51.2592675323290.8030.3861.3171100
8.27-76.7811.90.02348604090.9980.0070.02489.598.2

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Processing

Software
NameVersionClassification
PHENIX3500refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.85→76.155 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.56
RfactorNum. reflection% reflection
Rfree0.218 1583 4.96 %
Rwork0.197 --
obs0.198 31888 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 199.68 Å2 / Biso mean: 62.1073 Å2 / Biso min: 29.85 Å2
Refinement stepCycle: final / Resolution: 1.85→76.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 50 127 2021
Biso mean--51.18 54.19 -
Num. residues----234
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.90960.38861370.3491272799
1.9096-1.97790.28541460.27562707100
1.9779-2.05710.22211350.22852714100
2.0571-2.15070.23871250.20812730100
2.1507-2.26410.22231380.20652746100
2.2641-2.40590.22451330.21032758100
2.4059-2.59170.25231480.22132714100
2.5917-2.85250.22361520.23342762100
2.8525-3.26530.26961470.22052756100
3.2653-4.11390.20561720.18292775100
4.1139-76.1550.18331500.16422916100
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)
14.22081.50610.18164.6062-2.15345.7325-0.1970.0447-0.0547-0.21030.0401-0.153-0.11670.12220.14380.3952-0.06360.00960.2387-0.0420.378739.626229.354424.1989
22.9930.2201-3.54161.2992-0.20566.5463-0.26530.3357-0.0756-0.07070.05930.1173-0.091-0.53040.30960.3327-0.0332-0.04950.3132-0.05690.388520.910825.794531.8586
37.90711.423-3.32554.4354-0.08037.7471-0.251.0316-0.0702-0.5118-0.00530.14-0.3418-0.89630.22890.4174-0.0409-0.08310.5401-0.03390.355421.372325.539616.5633
48.3243-3.494-3.77526.66172.97772.2303-0.02770.81880.1889-0.6552-0.58140.7849-0.5869-1.80850.49280.45440.0129-0.20340.8759-0.05080.465414.987222.43311.9456
51.8595-1.808-0.783.38250.93272.96560.10630.0104-0.31520.0012-0.35890.46280.462-0.75740.19050.4558-0.261-0.01210.5757-0.10760.389819.75968.063514.6833
67.81861.7017.2052.17922.71057.52440.0592-0.97940.75870.30220.1438-0.0723-0.0844-0.4743-0.00510.5485-0.1575-0.00810.6394-0.10210.479819.521513.080625.5251
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 106 )A38 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 139 )A107 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 161 )A140 - 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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