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- PDB-5tn3: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 5tn3
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the estradiol derivative, (8S,9S,13S,14S)-17-((4-isopropylphenyl)amino)-13-methyl-7,8,9,11,12,13,14,15,16,17-decahydro-6H-cyclopenta[a]phenanthren-3-ol
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 / 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 / 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 / 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 / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid 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 / 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 / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / 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 / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific
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 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 / 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-7FS / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.543 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 13, 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)62,5386
Polymers61,7594
Non-polymers7792
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-29 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.620, 82.910, 58.590
Angle α, β, γ (deg.)90.00, 110.70, 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 298-554) / 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-7FS / (9beta,13alpha,17beta)-17-{[4-(propan-2-yl)phenyl]amino}estra-1(10),2,4-trien-3-ol


Mass: 389.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 39.89 % / Mosaicity: 1.304 °
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: 2.54→50 Å / Num. obs: 16465 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.91 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Rrim(I) all: 0.119 / Χ2: 0.662 / Net I/av σ(I): 14.857 / Net I/σ(I): 3.9 / Num. measured all: 109364
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.54-2.586.60.5750.9199.5
2.58-2.636.60.5360.907199.8
2.63-2.686.60.4860.932199.6
2.68-2.746.40.4440.922199.6
2.74-2.85.80.370.944198.6
2.8-2.8660.360.935198.8
2.86-2.9370.2880.9671100
2.93-3.0170.2440.9811100
3.01-3.170.2270.978199.9
3.1-3.270.1950.981199.8
3.2-3.316.90.1770.9861100
3.31-3.456.90.1410.992199.5
3.45-3.66.80.1320.988199.6
3.6-3.796.60.1130.992199.3
3.79-4.036.20.0980.992198.8
4.03-4.346.20.0920.992197.9
4.34-4.787.10.0840.9951100
4.78-5.4770.0750.995199.9
5.47-6.896.60.0760.997199.8
6.89-506.50.0560.998198.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.543→46.912 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1453 10.13 %
Rwork0.2007 --
obs0.2063 14344 87.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.543→46.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 40 62 4061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024108
X-RAY DIFFRACTIONf_angle_d0.485568
X-RAY DIFFRACTIONf_dihedral_angle_d17.4141523
X-RAY DIFFRACTIONf_chiral_restr0.035662
X-RAY DIFFRACTIONf_plane_restr0.003688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5433-2.63420.3043680.2488550X-RAY DIFFRACTION38
2.6342-2.73960.33071160.2482942X-RAY DIFFRACTION65
2.7396-2.86430.34091390.25811266X-RAY DIFFRACTION86
2.8643-3.01530.31661550.23611395X-RAY DIFFRACTION95
3.0153-3.20420.29491660.24261421X-RAY DIFFRACTION96
3.2042-3.45150.28341600.22531444X-RAY DIFFRACTION97
3.4515-3.79870.29541530.20181436X-RAY DIFFRACTION98
3.7987-4.3480.20821620.16631457X-RAY DIFFRACTION98
4.348-5.47670.21631630.16431479X-RAY DIFFRACTION100
5.4767-46.91990.19381710.17341501X-RAY DIFFRACTION99
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)
10.2052-0.6146-0.40251.73670.23231.02360.2399-0.39162.0806-0.4152-0.4092-0.0845-0.9660.06470.26940.60241.099-0.6859-0.09280.59880.05411.339319.7341-4.3559
23.21691.36090.77230.6656-0.36594.3426-0.28870.7171-0.66710.04340.0563-0.90520.71150.29590.2010.4160.10080.10650.4115-0.13910.508621.0739-6.4553-7.2176
32.0622-0.0525-0.97541.2971.09092.41340.07630.13250.23960.060.0961-0.1484-0.29570.2379-0.140.2546-0.01210.04050.23720.01930.293816.9227.63942.1293
43.77773.466-3.43023.7127-1.96075.5661-0.362-0.3548-1.0658-0.304-0.3085-0.06991.27380.43120.41570.3748-0.10770.08090.1358-0.08290.375811.4099-9.8478-3.1919
53.22040.7226-0.62824.67390.49923.9714-0.0527-0.1023-0.16060.053-0.0723-0.13810.3610.10540.10630.21070.07190.05690.26970.03630.20637.7759-0.50116.0743
62.5-0.1037-0.11271.8401-0.16013.22770.20040.03690.1616-0.2271-0.2201-0.0474-0.073-0.21160.05720.34320.1076-0.02540.3149-0.01040.2413.40066.85878.5891
77.0522-0.08452.44135.0369-1.09092.7471-0.4066-0.77280.5510.0092-0.1268-0.81380.8680.92580.46890.38670.10580.08810.51950.06430.459727.77954.26529.0349
81.38480.52780.41370.64611.19492.55510.2135-0.2505-0.51040.25260.20360.25231.3437-0.1372-0.41250.7097-0.3515-0.15610.9187-0.06240.8139-19.0552-5.250421.6674
93.618-0.35431.52322.6251-0.67534.04050.6611-0.72990.07210.39010.50190.9644-0.1224-1.1331-0.7489-1.4365-0.12230.33670.6851-0.20820.8219-15.92434.759927.8834
104.05041.42321.45713.03480.43962.3688-0.4278-0.25190.1054-0.09150.1555-0.3108-0.37970.92080.36880.2936-0.06520.0150.7331-0.070.39147.55139.423744.3275
113.0604-0.4199-0.81693.7684-0.66823.7738-0.1636-0.6754-0.46120.0282-0.1473-0.21710.19560.34780.37050.29630.0334-0.02590.29850.01180.25995.86340.886837.7925
122.5995-1.0088-0.37511.3234-0.18571.5003-0.02910.1284-0.8533-0.1105-0.11830.330.5904-0.42110.26740.4545-0.20490.06380.4161-0.08980.564-9.1927-7.744326.6761
132.5455-0.4252-0.45830.7192-0.29793.03490.0037-0.1543-0.0714-0.0089-0.0885-0.18470.06330.05320.12190.2429-0.0347-0.02860.26850.01310.2213.61964.879130.0387
14-0.00410.0346-0.0026-0.0514-0.0023-0.00860.24960.0798-0.1801-0.47250.208-1.07460.22391.0403-0.30720.6806-0.31540.03131.1368-0.33040.686517.283115.520435.0542
155.51180.49130.37763.76191.00353.99490.0319-0.07760.9948-0.2797-0.157-0.5129-0.46180.25480.08880.4946-0.18770.10890.3505-0.00130.41218.467415.982124.9779
162.83630.33050.05614.36050.35642.6949-0.13880.4135-0.113-0.6597-0.0490.00570.2784-0.37410.1540.3673-0.11310.010.3977-0.04650.2348-3.44442.738621.5558
172.81990.4407-1.21140.7059-0.53444.1564-0.07130.5321-0.3549-0.4194-0.31140.63820.3204-1.22080.26830.3471-0.0202-0.05990.5761-0.04630.2952-11.33610.898716.0658
181.9203-0.0288-1.84052.07130.57633.7151-0.1814-0.05470.09620.15780.0114-0.1831-0.29280.29690.01470.2223-0.03690.01290.23840.00670.28226.33417.174620.1378
193.6039-0.7887-0.42223.26930.64365.9927-0.81360.1351-0.08260.40120.1255-0.1842-0.18711.57840.85760.63870.2466-0.09560.62770.03270.704114.7181-6.568732.8516
203.4018-1.4749-2.19054.34890.32611.5180.5218-0.6171.25080.6027-0.5818-0.56-0.45490.7985-0.03250.5913-0.20820.02410.4762-0.0110.559826.42317.64161.92
212.2220.95991.42422.13430.06551.0475-0.445-0.5361-0.7882-0.0630.210.01050.7712-0.44360.12180.8041-0.1363-0.00640.4270.03740.49090.1364-13.795435.5646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 303 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 394 )
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 411 )
5X-RAY DIFFRACTION5chain 'A' and (resid 412 through 470 )
6X-RAY DIFFRACTION6chain 'A' and (resid 471 through 531 )
7X-RAY DIFFRACTION7chain 'A' and (resid 532 through 548 )
8X-RAY DIFFRACTION8chain 'B' and (resid 304 through 311 )
9X-RAY DIFFRACTION9chain 'B' and (resid 312 through 321 )
10X-RAY DIFFRACTION10chain 'B' and (resid 322 through 338 )
11X-RAY DIFFRACTION11chain 'B' and (resid 339 through 362 )
12X-RAY DIFFRACTION12chain 'B' and (resid 363 through 371 )
13X-RAY DIFFRACTION13chain 'B' and (resid 372 through 407 )
14X-RAY DIFFRACTION14chain 'B' and (resid 408 through 420 )
15X-RAY DIFFRACTION15chain 'B' and (resid 421 through 438 )
16X-RAY DIFFRACTION16chain 'B' and (resid 439 through 465 )
17X-RAY DIFFRACTION17chain 'B' and (resid 466 through 496 )
18X-RAY DIFFRACTION18chain 'B' and (resid 497 through 531 )
19X-RAY DIFFRACTION19chain 'B' and (resid 532 through 549 )
20X-RAY DIFFRACTION20chain 'C' and (resid 686 through 696 )
21X-RAY DIFFRACTION21chain 'D' and (resid 688 through 697 )

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