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- PDB-3uud: Crystal structure of hERa-LBD (Y537S) in complex with estradiol -

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Basic information

Entry
Database: PDB / ID: 3uud
TitleCrystal structure of hERa-LBD (Y537S) in complex with estradiol
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsHORMONE RECEPTOR / Ligand-binding domain of nuclear hormone receptor
Function / homology
Function and homology information


positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / steroid hormone receptor signaling pathway / 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 / nuclear estrogen receptor activity / hypothalamus development / male mating behavior / Developmental Lineage of Mammary Gland Alveolar Cells ...positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / steroid hormone receptor signaling pathway / 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 / nuclear estrogen receptor activity / hypothalamus development / male mating behavior / Developmental Lineage of Mammary Gland Alveolar Cells / progesterone receptor signaling pathway / TFIIB-class transcription factor binding / negative regulation of smooth muscle cell apoptotic process / response to progesterone / Synthesis of bile acids and bile salts / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cerebellum development / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / Mitochondrial unfolded protein response (UPRmt) / protein-lysine-acetyltransferase activity / nuclear retinoid X receptor binding / Nuclear signaling by ERBB4 / lactation / positive regulation of neuron differentiation / estrous cycle / estrogen receptor signaling pathway / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / RNA polymerase II preinitiation complex assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to hormone stimulus / positive regulation of nitric-oxide synthase activity / peroxisome proliferator activated receptor signaling pathway / steroid binding / Regulation of lipid metabolism by PPARalpha / stem cell differentiation / protein localization to chromatin / positive regulation of adipose tissue development / bile acid and bile salt transport / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 14-3-3 protein binding / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / male gonad development / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / hippocampus development / nuclear estrogen receptor binding / nuclear 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / cerebral cortex development / euchromatin / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / beta-catenin binding / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coactivator binding / positive regulation of nitric oxide biosynthetic process / transcription coregulator activity / 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 / transcription regulator complex / positive regulation of cytosolic calcium ion concentration / HATs acetylate histones / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding
Similarity search - Function
Nuclear receptor coactivator 1 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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
ESTRADIOL / Estrogen receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,38010
Polymers60,4974
Non-polymers8836
Water6,810378
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-31 kcal/mol
Surface area20350 Å2
MethodPISA
2
A: Estrogen receptor
C: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6134
Polymers30,2492
Non-polymers3642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area11770 Å2
MethodPISA
3
B: Estrogen receptor
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7676
Polymers30,2492
Non-polymers5194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-9 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.230, 82.010, 58.930
Angle α, β, γ (deg.)90.00, 111.06, 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: 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
#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

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Protein/peptide , 1 types, 2 molecules CD

#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

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Non-polymers , 4 types, 384 molecules

#4: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM Li2SO4, 100 mM Tris pH 8.5, 30% PEG 4000, 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: 1.6→45.7 Å / Num. all: 65563 / Num. obs: 65563 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.43 Å2 / Rsym value: 0.039 / Net I/σ(I): 18.19
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.53 / Num. unique all: 9907 / Rsym value: 0.47 / % possible all: 99.8

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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: 1.6→45.675 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 3278 5 %Random
Rwork0.1658 ---
obs0.1672 65563 99.66 %-
all-65563 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.048 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7476 Å2-0 Å20.8555 Å2
2--0.2271 Å20 Å2
3----1.9747 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 62 378 4354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084179
X-RAY DIFFRACTIONf_angle_d1.0215689
X-RAY DIFFRACTIONf_dihedral_angle_d17.7741582
X-RAY DIFFRACTIONf_chiral_restr0.07679
X-RAY DIFFRACTIONf_plane_restr0.004701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6-1.62390.23381420.237726932693100
1.6239-1.64930.24721410.23626942694100
1.6493-1.67630.29981450.236227522752100
1.6763-1.70520.25321400.229326582658100
1.7052-1.73620.27021430.229227072707100
1.7362-1.76960.29481430.208527232723100
1.7696-1.80570.22311420.197727022702100
1.8057-1.8450.21411420.188626832683100
1.845-1.88790.24921410.176726952695100
1.8879-1.93510.21461430.169527142714100
1.9351-1.98750.19351430.167827032703100
1.9875-2.04590.1981420.166327052705100
2.0459-2.1120.19051430.161327262726100
2.112-2.18750.20091420.157126952695100
2.1875-2.2750.18431440.156527252725100
2.275-2.37860.17291430.154827172717100
2.3786-2.5040.20251420.161127042704100
2.504-2.66080.20851430.166627102710100
2.6608-2.86620.20641430.165827122712100
2.8662-3.15460.19221430.160427262726100
3.1546-3.61090.16011430.150827212721100
3.6109-4.54880.16051440.133427332733100
4.5488-45.69360.19341410.17582687268796
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)
10.6734-0.1312-0.37630.2228-0.00021.3833-0.1332-0.1399-0.03850.10540.04450.00480.0750.0880.08210.10440.00150.02860.0446-0.00260.00812.23242.4996.1616
20.25320.0385-0.39220.02840.03281.7619-0.00610.0226-0.0003-0.0446-0.018-0.0107-0.0475-0.06770.01830.1101-0.00090.0320.0316-0.01480.034312.99126.0899-5.9686
30.0026-0.0265-0.03340.91061.14551.4441-0.2366-0.0505-0.2171-0.25530.2063-0.0901-0.2010.30740.04690.26320.03490.08580.2290.08130.139924.0342-8.09985.8545
40.9623-0.1201-0.49780.06420.2470.7964-0.09210.15760.2078-0.1546-0.04720.0645-0.09440.04350.02730.0890.02850.10180.0309-0.0097-0.097425.27813.7417-28.661
51.0378-0.1671-0.67930.14910.2010.8848-0.02040.0409-0.0389-0.0298-0.02810.00670.0622-0.10070.04510.12130.01110.02060.0294-0.0028-0.000716.42711.7004-20.2402
60.341-0.74750.38242.6053-0.29320.73550.1073-0.05260.1197-0.0921-0.2036-0.4728-0.02130.08840.10190.14420.00840.04820.16240.04760.205638.50073.5642-19.4503
71.85641.5015-1.40682.2765-2.20822.1438-0.45-0.1602-0.558-0.76640.0745-0.36240.6024-0.00750.37730.29360.03030.13170.09320.09350.226711.2359-14.71647.945
80.9040.4461-0.39260.77940.42560.85610.1316-0.05050.2754-0.1454-0.0793-0.0789-0.10520.1162-0.0580.1881-0.0580.16680.11830.00530.252837.647916.336-25.7015
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 C
8X-RAY DIFFRACTION8chain D

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