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- PDB-5tm5: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 5tm5
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the OBHS-ASC compound, 5-(4-((1R,4S,6R)-6-((4-bromophenoxy)sulfonyl)-3-(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-2-en-2-yl)phenoxy)pentanoic acid
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose 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 / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / 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 / 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 / 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 / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / 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 / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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-7EV / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsNwachukwu, J.C. / Wright, N.J. / Erumbi, R. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Izard, T. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9906
Polymers61,7594
Non-polymers1,2312
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-29 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.464, 82.666, 59.029
Angle α, β, γ (deg.)90.00, 110.82, 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: 29299.535 Da / Num. of mol.: 2 / Fragment: ligand-binding domain, UNP residues 125-381 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2
Fragment: Nuclear receptor-interacting peptide, UNP residues 686-698
Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-7EV / 5-{4-[(1S,4S,5R)-5-[(4-bromophenoxy)sulfonyl]-3-(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-2-en-2-yl]phenoxy}pentanoic acid


Mass: 615.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H27BrO8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.94 % / Mosaicity: 0.731 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
RadiationMonochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.24→47.034 Å / Num. obs: 23822 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.72 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 5
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.606 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→47.03 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.9
RfactorNum. reflection% reflection
Rfree0.232 1900 8.43 %
Rwork0.187 --
obs0.191 22541 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 63.14 Å2
Refinement stepCycle: LAST / Resolution: 2.24→47.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3837 0 50 79 3966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024001
X-RAY DIFFRACTIONf_angle_d0.4765426
X-RAY DIFFRACTIONf_dihedral_angle_d15.0942410
X-RAY DIFFRACTIONf_chiral_restr0.034642
X-RAY DIFFRACTIONf_plane_restr0.003671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2357-2.29160.32761100.24691247X-RAY DIFFRACTION80
2.2916-2.35360.29161330.24141335X-RAY DIFFRACTION85
2.3536-2.42280.29111130.22741405X-RAY DIFFRACTION88
2.4228-2.5010.27281360.21871425X-RAY DIFFRACTION92
2.501-2.59040.27711270.22371449X-RAY DIFFRACTION92
2.5904-2.69410.2491390.19891470X-RAY DIFFRACTION92
2.6941-2.81670.29881310.21281420X-RAY DIFFRACTION91
2.8167-2.96520.25261390.22181528X-RAY DIFFRACTION97
2.9652-3.15090.25231470.20681537X-RAY DIFFRACTION98
3.1509-3.39420.22481430.20731565X-RAY DIFFRACTION99
3.3942-3.73560.2561470.1921558X-RAY DIFFRACTION98
3.7356-4.27580.21671440.15981525X-RAY DIFFRACTION96
4.2758-5.38590.19221450.15541575X-RAY DIFFRACTION99
5.3859-47.04410.19721460.16881602X-RAY DIFFRACTION98
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)
11.3216-0.17340.4750.20370.14942.1050.3110.0519-0.24190.30640.2353-0.34320.25661.32270.75170.36120.1097-0.01090.96280.12140.683323.75470.84229.5119
20.97140.7027-0.75710.8121-0.2890.52280.00920.5298-0.419-0.14190.2250.4347-0.0031-0.84910.00380.4093-0.0374-0.02360.82570.08710.4191-1.13039.161110.6756
31.28951.15160.26480.8653-0.42723.8493-0.10430.15090.0751-0.76770.0145-0.1731.7236-0.6903-0.30760.412-0.11880.02530.55450.00850.40911.67660.118717.3564
41.94470.61480.0230.70071.14352.7738-0.23680.0177-0.3584-0.2036-0.1984-0.02590.9112-0.0271-1.00740.57460.07610.14970.32680.04050.37096.559-3.300728.1138
50.44840.04010.0714-0.02480.0350.3515-0.11520.71670.3245-0.33990.43070.1554-1.4733-0.21040.00910.54370.04620.0120.59260.07590.47170.235516.276318.7551
60.286-0.0039-0.4122-0.00670.0280.7410.38310.26640.0250.34610.5721-0.2126-0.3288-0.74991.34330.15750.44650.10981.42950.69451.348-13.257814.239921.1399
70.7767-0.1263-0.6773-0.13120.48123.931-0.0546-0.0566-0.12770.45380.1530.3008-0.57320.0620.0050.35880.03720.02260.26650.06760.39485.089211.087430.4299
86.26681.30311.76860.29620.32590.4676-0.3306-0.88220.86971.5034-0.82050.54520.57010.1428-0.40611.311-0.00040.2420.9176-0.04830.62946.172-10.946139.8553
91.02481.4878-0.94122.88740.59414.55320.2725-0.4724-0.06620.6469-0.8645-1.00590.42021.9824-0.82270.25260.0488-0.07840.73460.18080.475918.79452.539238.786
101.00950.0304-1.73310.3357-0.63672.9777-0.10810.15630.12760.1654-0.03620.2587-0.2742-0.24760.00020.2946-0.0054-0.03170.294-0.01550.35720.79136.946435.196
110.29490.21930.19770.26170.54771.021-0.81680.4734-0.2378-0.03420.0666-0.44211.0741-0.9972-0.19030.6973-0.28910.08520.7936-0.10820.7522-7.3756-7.135421.7651
120.73851.4946-0.98363.664-1.36281.65030.7046-0.97230.98780.7971-0.43120.8629-0.80011.01750.46020.8017-0.3377-0.03970.6705-0.12760.61525.355918.709959.8462
131.35370.25360.73320.628-0.34640.59630.1663-1.112-0.29720.0578-0.68720.46110.1465-0.6246-0.23540.5085-0.25080.0790.619-0.04640.5116-14.3767-6.91762.2621
141.399-0.1343-1.3406-0.02170.03490.8033-0.0002-0.3609-0.13920.11720.0907-0.14880.1355-0.45680.00070.4992-0.11280.05310.4126-0.01580.4206-14.90481.426855.9695
151.7281-0.1769-1.15690.4960.1170.55750.18130.17080.46220.0596-0.1540.0651-0.2855-0.2186-00.4194-0.00770.0720.3060.01710.4237-6.943610.633950.8518
166.23421.3446-0.68274.34041.0333.0054-1.5654-1.7075-1.5910.4208-0.26810.79251.78060.4947-2.59480.8137-0.06280.2477-0.0710.10790.5378-7.5013-12.333154.4096
172.40250.864-1.86441.25060.18822.78280.09990.0092-0.28350.0057-0.1526-0.0880.29090.3022-0.00090.3865-0.04360.00260.3375-0.01170.33011.31791.684949.0649
182.68430.9531-0.78420.6991-0.59832.97890.261-0.18260.00220.2296-0.38430.06890.09970.1727-0.15980.3264-0.0469-0.03140.2847-0.00490.29283.70365.547546.6775
190.06510.33630.32620.70320.73560.70570.43950.2640.43590.3534-0.11210.36690.4689-0.14390.0080.4505-0.08210.00140.6646-0.01380.6283-21.20254.01145.9091
200.9778-0.19060.89040.0499-0.22851.0415-0.18671.0361-1.5231-0.62810.18510.05830.54060.34260.06561.1027-0.06810.10790.4315-0.13110.67266.0276-14.426619.5719
212.9417-1.7664-3.53222.6012.59534.52650.90830.3896-0.83330.6436-1.09570.31710.4959-1.8317-0.34430.77440.10720.24950.68960.08440.995-19.196316.868153.8893
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 305 THROUGH 321 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 322 THROUGH 338 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 339 THROUGH 363 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 364 THROUGH 394 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 395 THROUGH 411 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 412 THROUGH 420 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 421 THROUGH 455 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 456 THROUGH 469 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 470 THROUGH 496 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 497 THROUGH 531 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 532 THROUGH 548 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 304 THROUGH 321 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 322 THROUGH 338 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 339 THROUGH 362 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 363 THROUGH 394 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 395 THROUGH 421 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 422 THROUGH 472 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 473 THROUGH 531 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 532 THROUGH 548 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 688 THROUGH 696 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 687 THROUGH 696 )

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