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- PDB-4tuz: Crystal structure of hERa-LBD (Y537S) in complex with alpha-zearalenol -

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Basic information

Entry
Database: PDB / ID: 4tuz
TitleCrystal structure of hERa-LBD (Y537S) in complex with alpha-zearalenol
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsNUCLEAR PROTEIN / nuclear hormone receptor ligand binding domain endocrine disruptor environmental compound
Function / homology
Function and homology information


labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / RUNX1 regulates transcription of genes involved in WNT signaling ...labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / hypothalamus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / male mating behavior / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / androgen metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / steroid binding / : / 14-3-3 protein binding / lactation / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / hippocampus development / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / Heme signaling
Similarity search - Function
Nuclear receptor coactivator 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily ...Nuclear receptor coactivator 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / : / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-36J / Estrogen receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDelfosse, V. / Grimaldi, M. / Bourguet, W.
Funding support France, 1items
OrganizationGrant numberCountry
ANR CESA2010 CESA 004 02 France
CitationJournal: Acta Pharmacol. Sin. / Year: 2015
Title: A structural perspective on nuclear receptors as targets of environmental compounds.
Authors: Delfosse, V. / Maire, A.L. / Balaguer, P. / Bourguet, W.
History
DepositionJun 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Feb 27, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Feb 19, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site_gen
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_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 2023Group: 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
F: Nuclear receptor coactivator 1
G: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,47312
Polymers61,3404
Non-polymers1,1338
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-30 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.960, 83.430, 58.770
Angle α, β, γ (deg.)90.00, 108.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29070.217 Da / Num. of mol.: 1 / Fragment: Residues 302-552 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET15b / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P03372
#2: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29086.217 Da / Num. of mol.: 1 / Fragment: Residues 302-552 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372

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Protein/peptide , 1 types, 2 molecules FG

#3: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: Residues 686-698 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788*PLUS, histone acetyltransferase

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Non-polymers , 4 types, 273 molecules

#4: Chemical ChemComp-36J / (3S,7R,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9,10-octahydro-1H-2-benzoxacyclotetradecin-1-one


Mass: 320.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O5
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 300-340 mM NaCl 100 mM Hepes 24-32 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→46.52 Å / Num. obs: 40075 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rsym value: 0.05 / Net I/σ(I): 13.85
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.68 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX(phenix.refine: 1.6.4_486)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UUD

3uud


Resolution: 1.9→46.52 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 2004 5 %Random selection
Rwork0.1782 ---
obs0.1796 40069 99.23 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.614 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.825 Å2-0 Å24.7483 Å2
2--3.5414 Å2-0 Å2
3---1.2836 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3889 0 78 265 4232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054180
X-RAY DIFFRACTIONf_angle_d0.8535685
X-RAY DIFFRACTIONf_dihedral_angle_d17.2431576
X-RAY DIFFRACTIONf_chiral_restr0.058670
X-RAY DIFFRACTIONf_plane_restr0.003712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.28681430.2452722X-RAY DIFFRACTION99
1.9475-2.00020.26371420.23252690X-RAY DIFFRACTION100
2.0002-2.05910.26211430.21442715X-RAY DIFFRACTION100
2.0591-2.12550.23571430.18922726X-RAY DIFFRACTION100
2.1255-2.20150.21881410.19042685X-RAY DIFFRACTION99
2.2015-2.28960.21951450.18622739X-RAY DIFFRACTION99
2.2896-2.39380.23641430.18552717X-RAY DIFFRACTION99
2.3938-2.520.20371420.18232710X-RAY DIFFRACTION99
2.52-2.67790.20411450.17872745X-RAY DIFFRACTION99
2.6779-2.88460.19211420.17382702X-RAY DIFFRACTION99
2.8846-3.17490.2091410.17092688X-RAY DIFFRACTION98
3.1749-3.63410.18811440.17232733X-RAY DIFFRACTION99
3.6341-4.5780.18671430.15062718X-RAY DIFFRACTION98
4.578-46.54150.20821470.18622775X-RAY DIFFRACTION99

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