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- PDB-5tm6: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 5tm6
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the OBHS-ASC compound, 6-(4-((1R,4S,6R)-6-((4-bromophenoxy)sulfonyl)-3-(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-2-en-2-yl)phenoxy)hexanoic 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / 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 / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7J9 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.542 Å
AuthorsNwachukwu, J.C. / 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)63,0186
Polymers61,7594
Non-polymers1,2592
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-28 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.529, 81.603, 58.251
Angle α, β, γ (deg.)90.000, 110.970, 90.000
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 / 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 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-7J9 / 6-{4-[(1S,4S,6R)-6-[(4-bromophenoxy)sulfonyl]-3-(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-2-en-2-yl]phenoxy}hexanoic acid


Mass: 629.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H29BrO8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.96 Å3/Da / Density % sol: 37.23 % / Mosaicity: 0.811 °
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: Apr 24, 2014
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: 2.53→46.36 Å / Num. obs: 15364 / % possible obs: 97.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 44.29 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.043 / Rrim(I) all: 0.115 / Χ2: 0.662 / Net I/av σ(I): 15.938 / Net I/σ(I): 4 / Num. measured all: 105230
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.53-2.576.50.6670.914197.6
2.57-2.626.70.560.932197.8
2.62-2.676.60.4910.941197.4
2.67-2.736.50.4570.948198.1
2.73-2.786.20.4640.939191.2
2.78-2.856.70.3920.953195.1
2.85-2.927.20.2820.982198.9
2.92-37.20.240.986199.4
3-3.097.10.2120.985199.1
3.09-3.197.20.1960.989199.3
3.19-3.37.10.1760.987199.2
3.3-3.4370.1310.995199.5
3.43-3.5970.1250.993199.2
3.59-3.786.70.1050.994199
3.78-4.026.20.0980.994196.8
4.02-4.336.80.0940.994192.5
4.33-4.767.20.0840.995199.6
4.76-5.457.10.080.995199.8
5.45-6.866.80.080.992198.6
6.86-506.90.0490.998194

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.542→46.36 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.75
RfactorNum. reflection% reflection
Rfree0.2448 1448 9.89 %
Rwork0.1885 --
obs0.194 14646 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 188.23 Å2 / Biso mean: 66.8919 Å2 / Biso min: 21.74 Å2
Refinement stepCycle: final / Resolution: 2.542→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 50 37 3974
Biso mean--66 41.94 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024051
X-RAY DIFFRACTIONf_angle_d0.4565493
X-RAY DIFFRACTIONf_chiral_restr0.031647
X-RAY DIFFRACTIONf_plane_restr0.003680
X-RAY DIFFRACTIONf_dihedral_angle_d14.4972431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5421-2.6330.30571270.24351150127781
2.633-2.73840.30381440.24511222136687
2.7384-2.8630.35031230.24991228135186
2.863-3.01390.27881510.20981311146293
3.0139-3.20270.28191370.21521367150495
3.2027-3.44990.25711530.21081378153197
3.4499-3.7970.25861580.18861372153098
3.797-4.34610.221470.16591335148294
4.3461-5.47420.20521530.16091448160199
5.4742-46.36780.21791550.1711387154296
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)
10.5205-0.3820.55740.6804-0.40060.71750.46920.25740.2346-0.18520.29420.0729-0.0631-0.71631.60130.17910.8982-0.68180.61580.8647-0.76521.216519.0779-4.6873
20.195-0.06670.19450.26940.02690.15310.05190.6921-0.3637-0.46250.0275-0.0025-0.59390.35730.3040.39320.3260.04170.3860.19570.35120.3254-4.7482-6.8427
31.0628-0.0152-0.9950.4202-0.09460.80980.1629-0.09120.1360.0512-0.0818-0.1211-0.0837-0.02420.00010.2840.03550.04520.25160.01420.298616.30146.96251.9866
41.709-0.0174-0.520.591-0.82481.4205-0.75230.5019-1.0776-0.115-0.1883-0.63611.0009-0.04-0.37910.7164-0.03450.15510.2728-0.05780.577415.55-12.45431.3126
51.3041-0.5069-0.85280.8736-0.00432.2234-0.39520.47710.16150.4074-0.35990.15161.1997-0.3249-0.36550.7119-0.02480.05210.2088-0.03360.38596.507-7.83476.8115
60.1963-0.0397-0.22960.03440.08140.23540.19170.2620.0551-0.2155-0.19750.13280.3373-0.56520.00130.34660.127-0.02530.427-0.02740.32932.96327.20021.5246
7-0.0111-0.00830.01420.02050.0008-0.0016-0.1358-0.49980.31930.4540.39910.4274-0.09410.32280.00011.0894-0.13010.12210.634-0.02280.690610.858117.471415.5658
80.6624-0.2977-0.52810.42840.10621.85570.3060.67020.0843-0.1071-0.4430.08420.0182-0.3878-0.06580.36610.1052-0.01280.4929-0.01670.32223.10086.0668.5023
91.2411-0.4408-1.16280.13130.37171.26210.29970.05310.7311-0.00860.2905-0.5043-0.41710.41280.15280.24370.0148-0.08760.6284-0.0350.517127.7224.64729.316
101.3470.46970.10130.34120.26851.54380.02670.05150.21880.36180.4661-0.08770.3096-0.6760.30750.3326-0.19960.03950.7713-0.12450.6321-17.09110.881125.4416
110.2722-0.3291-0.22460.7516-0.08460.45290.1259-0.43370.04510.1398-0.077-0.1832-0.13551.01180.07250.6131-0.00810.15470.7293-0.09660.43387.102910.03643.9101
121.1137-0.3628-1.10770.0901-0.33921.6852-0.4865-0.008-0.38810.04110.2050.22250.58150.1317-0.0160.44870.01410.07790.26280.00650.34612.71582.082632.2262
130.22670.07-0.12830.0115-0.0520.2165-0.0513-0.1144-0.3456-0.20150.2326-0.091-0.35740.31260.15-0.1635-0.7247-0.07090.587-0.83350.95617.35515.686434.8248
140.0960.0060.05840.06410.51341.5991-0.24180.01080.53380.05520.0596-0.0996-1.70020.3994-0.03680.4873-0.15410.1170.3504-0.02820.43128.353116.102124.9413
151.26790.0316-0.9060.7033-0.32960.8774-0.22090.5514-0.43910.1862-0.1183-0.22440.0545-0.8188-0.08260.2786-0.0115-0.06280.4198-0.05560.3174-5.56317.428323.7938
160.4539-0.01360.14870.00820.01360.0351-0.21340.05730.5352-0.19920.0313-0.3140.141-0.1972-0.2091.4107-0.07060.39360.9731-0.01520.64870.7019-11.642814.9352
170.5851-0.2215-0.89810.32640.6031.86220.03670.12350.0415-0.173-0.26450.04980.1223-0.5831-0.01160.28540.0280.01030.4275-0.04920.3301-1.32495.404818.3406
180.02890.02230.0491-0.0412-0.00480.0167-0.1649-0.2359-0.690.17660.11940.40210.1290.3481-00.86360.2707-0.06960.63290.05880.72614.3416-5.865733.4819
190.1394-0.2126-0.09860.51930.3120.30910.14820.241-0.2888-0.5321-0.408-0.0437-0.39640.5438-0.07210.559-0.05420.30250.66570.03931.146325.733517.61411.4888
200.03970.11920.06340.44330.41510.4735-0.3208-0.1607-0.23180.13460.122-0.7364-0.1308-0.31080.0370.93690.00920.19720.60520.20270.64640.2904-13.44435.8447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 321 )A304 - 321
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A322 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 397 )A339 - 397
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 420 )A398 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 438 )A421 - 438
6X-RAY DIFFRACTION6chain 'A' and (resid 439 through 455 )A439 - 455
7X-RAY DIFFRACTION7chain 'A' and (resid 456 through 472 )A456 - 472
8X-RAY DIFFRACTION8chain 'A' and (resid 473 through 531 )A473 - 531
9X-RAY DIFFRACTION9chain 'A' and (resid 532 through 548 )A532 - 548
10X-RAY DIFFRACTION10chain 'B' and (resid 304 through 321 )B304 - 321
11X-RAY DIFFRACTION11chain 'B' and (resid 322 through 338 )B322 - 338
12X-RAY DIFFRACTION12chain 'B' and (resid 339 through 407 )B339 - 407
13X-RAY DIFFRACTION13chain 'B' and (resid 408 through 420 )B408 - 420
14X-RAY DIFFRACTION14chain 'B' and (resid 421 through 438 )B421 - 438
15X-RAY DIFFRACTION15chain 'B' and (resid 439 through 455 )B439 - 455
16X-RAY DIFFRACTION16chain 'B' and (resid 456 through 468 )B456 - 468
17X-RAY DIFFRACTION17chain 'B' and (resid 469 through 531 )B469 - 531
18X-RAY DIFFRACTION18chain 'B' and (resid 532 through 548 )B532 - 548
19X-RAY DIFFRACTION19chain 'C' and (resid 687 through 696 )C687 - 696
20X-RAY DIFFRACTION20chain 'D' and (resid 688 through 697 )D688 - 697

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