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- PDB-3uua: Crystal structure of hERa-LBD (Y537S) in complex with bisphenol-AF -

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Basic information

Entry
Database: PDB / ID: 3uua
TitleCrystal structure of hERa-LBD (Y537S) in complex with bisphenol-AF
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsHORMONE RECEPTOR / Ligand-binding domain of nuclear hormone receptor
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 / 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 ...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 / 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 / male mating behavior / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / hypothalamus development / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / androgen metabolic process / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / response to retinoic acid / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / estrous cycle / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / histone acetyltransferase / RNA polymerase II preinitiation complex assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / positive regulation of adipose tissue development / : / steroid binding / lactation / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / TBP-class protein binding / cerebellum development / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription coregulator binding / transcription corepressor binding / stem cell differentiation / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / Regulation of RUNX2 expression and activity / transcription coactivator binding / male gonad development / nuclear receptor activity / Ovarian tumor domain proteases / : / positive regulation of fibroblast proliferation
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-0CZ / Estrogen receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDelfosse, V. / Grimaldi, M. / Bourguet, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and mechanistic insights into bisphenols action provide guidelines for risk assessment and discovery of bisphenol A substitutes.
Authors: Delfosse, V. / Grimaldi, M. / Pons, J.L. / Boulahtouf, A. / le Maire, A. / Cavailles, V. / Labesse, G. / Bourguet, W. / Balaguer, P.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / 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
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)61,1546
Polymers60,4814
Non-polymers6722
Water2,594144
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-29 kcal/mol
Surface area19790 Å2
MethodPISA
2
A: Estrogen receptor
F: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5693
Polymers30,2332
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-9 kcal/mol
Surface area11760 Å2
MethodPISA
3
B: Estrogen receptor
G: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5853
Polymers30,2492
Non-polymers3361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-9 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.700, 81.950, 58.880
Angle α, β, γ (deg.)90.00, 110.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28640.742 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 28656.742 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#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: Coactivator peptide SRC-1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#4: Chemical ChemComp-0CZ / 4,4'-(1,1,1,3,3,3-hexafluoropropane-2,2-diyl)diphenol / BISPHENOL AF


Mass: 336.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10F6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 300 mM NaCl, 100 mM Hepes pH 7.75, 32% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.05→46.6 Å / Num. all: 30405 / Num. obs: 30405 / % possible obs: 99.52 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 32.75 Å2 / Rsym value: 0.052 / Net I/σ(I): 15.11
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.68 / Num. unique all: 4742 / Rsym value: 0.475 / % possible all: 99.5

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Processing

Software
NameClassification
MxCuBEdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L03

3l03


Resolution: 2.05→46.6 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1521 5 %Random
Rwork0.1897 ---
obs0.1918 30405 99.52 %-
all-30405 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.801 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8667 Å2-0 Å27.2168 Å2
2--2.1087 Å20 Å2
3----3.9754 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 46 144 3986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043947
X-RAY DIFFRACTIONf_angle_d0.7625361
X-RAY DIFFRACTIONf_dihedral_angle_d17.8541432
X-RAY DIFFRACTIONf_chiral_restr0.051642
X-RAY DIFFRACTIONf_plane_restr0.003659
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.05-2.11620.32531360.255325932593100
2.1162-2.19180.31291390.228526372637100
2.1918-2.27960.24951390.218626252625100
2.2796-2.38330.26771370.210726182618100
2.3833-2.50890.27691370.213826012601100
2.5089-2.66610.27051390.216626442644100
2.6661-2.8720.24891380.216526202620100
2.872-3.16090.22421380.19732626262699
3.1609-3.61810.24631390.17662631263199
3.6181-4.55790.18821390.15772633263399
4.5579-46.61160.20151400.1772656265699
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)
11.27420.0435-0.81790.2749-0.28812.8184-0.2442-0.1822-0.18610.06070.0373-0.0260.27690.07870.14670.1829-0.01140.01270.172-0.01450.140111.33912.65626.0791
21.761-0.2971-0.78380.81670.03893.87170.1118-0.02380.024-0.019-0.1783-0.03480.0807-0.13810.0750.1238-0.00040.00630.1194-0.02880.136111.99135.9553-5.8623
30.6142-0.6562-0.15380.9007-0.28674.4091-0.6522-0.1322-0.31170.274-0.1310.21240.03811.12620.51230.40960.12370.01390.50480.13610.308724.7408-6.99975.9964
41.0231-0.5187-1.4440.72771.05542.1189-0.0010.24160.09080.0639-0.0761-0.1041-0.1063-0.0410.03450.09430.0313-0.01240.12220.00540.112424.75084.2347-28.1641
52.3385-0.74-1.20621.14530.33812.6369-0.00130.1879-0.15910.1397-0.1690.04160.1219-0.29440.14870.11840.0198-0.00250.1084-0.00940.10416.19581.5882-19.88
61.8923-1.0752-0.8320.95860.83491.46290.0602-0.17940.5932-0.06040.2152-0.58510.06590.8445-0.09650.10740.0151-0.02420.3543-0.00890.242537.74373.9545-18.2519
71.5416-0.6989-0.60060.48251.02433.874-0.1728-0.0508-0.85570.47450.3753-0.60060.73060.1331-0.22610.56590.02220.13440.20860.17370.452212.0571-14.54898.4502
80.8408-0.6685-0.35440.63440.34151.1563-0.13510.16680.3908-0.475-0.1316-0.4703-0.38250.3176-0.20660.324-0.07420.1330.2820.03030.567635.688416.8237-26.8412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 305:410
2X-RAY DIFFRACTION2chain A and resseq 411:532
3X-RAY DIFFRACTION3chain A and resseq 533:548
4X-RAY DIFFRACTION4chain B and resseq 305:410
5X-RAY DIFFRACTION5chain B and resseq 411:532
6X-RAY DIFFRACTION6chain B and resseq 533:548
7X-RAY DIFFRACTION7chain F
8X-RAY DIFFRACTION8chain G

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