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

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Basic information

Entry
Database: PDB / ID: 5tlx
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with 3,4-bis(4-hydroxyphenyl)thiophene 1,1-dioxide
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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / 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 / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus 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 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / 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-7EH / Chem-7G5 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 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

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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)63,41710
Polymers61,7594
Non-polymers1,6586
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-32 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.270, 81.950, 58.590
Angle α, β, γ (deg.)90.000, 110.890, 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, 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-7EH / 3-methyl-6-phenyl-3H-imidazo[4,5-b]pyridin-2-amine


Mass: 224.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N4
#4: Chemical
ChemComp-7G5 / 3,4-bis(4-hydroxyphenyl)-2,5-dihydro-1H-1lambda~6~-thiophene-1,1-dione


Mass: 302.345 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.97 Å3/Da / Density % sol: 37.59 % / Mosaicity: 0.713 °
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: Jul 27, 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: 2.103→50 Å / Num. obs: 27454 / % possible obs: 98.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.41 Å2 / Rmerge(I) obs: 0.093 / Net I/av σ(I): 28.364 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.11-2.155.40.654198
2.15-2.195.30.539195.1
2.19-2.236.20.573198.8
2.23-2.276.90.501199.4
2.27-2.326.90.439199.5
2.32-2.3870.367199.4
2.38-2.446.90.329199.3
2.44-2.56.90.281199.2
2.5-2.586.90.248199.1
2.58-2.666.90.205199.2
2.66-2.756.50.173197.8
2.75-2.866.10.151196.5
2.86-2.997.20.129199.4
2.99-3.157.20.116199.4
3.15-3.357.10.105199.2
3.35-3.6170.092198.7
3.61-3.976.50.086197.6
3.97-4.546.50.081196.3
4.54-5.7270.08199.6
5.72-506.50.067196.2

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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: 2.103→46.335 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.98
RfactorNum. reflection% reflection
Rfree0.2263 1716 7.23 %
Rwork0.1952 --
obs0.1975 23725 85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.47 Å2 / Biso mean: 49.9416 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 2.103→46.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 118 132 4133
Biso mean--76.19 40.38 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154139
X-RAY DIFFRACTIONf_angle_d0.9885621
X-RAY DIFFRACTIONf_chiral_restr0.059648
X-RAY DIFFRACTIONf_plane_restr0.005695
X-RAY DIFFRACTIONf_dihedral_angle_d17.9321514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1034-2.16530.3572410.295165069130
2.1653-2.23510.2882820.27221165124754
2.2351-2.3150.2931320.2541591172375
2.315-2.40770.28831510.25061939209090
2.4077-2.51730.25141510.21562009216093
2.5173-2.650.26531730.21912032220595
2.65-2.8160.25891640.22482030219494
2.816-3.03340.22731610.20792086224797
3.0334-3.33860.25041580.20782118227698
3.3386-3.82150.21971710.18092113228498
3.8215-4.81390.19221660.15652115228197
4.8139-46.34640.18591660.16992161232798
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)
11.1776-0.45530.33331.20670.01370.1082-0.14280.09490.49810.08720.11450.1312-0.3782-0.20860.65010.47110.7838-0.27920.87810.33750.34370.458118.2618-5.1315
21.46821.26460.36062.6762-2.50995.129-0.266-0.0989-0.5978-0.463-0.4094-0.65691.22220.68670.47010.52650.23390.18320.44650.1140.410921.0319-5.2633-6.6839
33.59180.6734-0.78793.42080.8864.46970.1470.13470.34-0.0801-0.0233-0.1685-0.30410.16390.0240.12130.01940.01620.16890.04130.223416.54537.9132.4053
44.56142.7751-0.61764.0191-0.25122.3708-0.30350.4869-0.4179-0.3038-0.13620.39640.4679-0.63970.35510.447-0.09860.07480.278-0.12770.407710.2114-8.71-3.3344
51.3235-0.33580.1822.1803-0.66422.85-0.1296-0.1432-0.98090.35010.0764-0.46591.63290.18970.12340.94680.07460.12790.30550.02010.722917.8982-14.20414.74
67.6177-2.4380.14466.4835-0.82096.3561-0.19890.1128-0.99940.3527-0.37280.2231.1347-0.55370.18960.505-0.09210.15520.2361-0.04770.37126.3686-7.61467.1394
72.6914-0.9401-0.87885.30670.02934.93210.02290.76850.0855-0.3226-0.16120.4297-0.0008-0.8520.27510.11490.0869-0.00930.38040.00470.16942.52037.23651.6765
84.0814-1.6532-0.74282.26451.42972.60770.2761-1.01331.53831.09240.430.2223-1.1687-0.0026-0.47140.5470.04580.07990.389-0.04880.46999.857517.249515.3173
94.6705-0.14481.95031.235-0.55053.74650.02720.69420.6431-0.5286-0.2230.4697-0.5222-0.38940.78180.3470.3114-0.06880.71740.04180.3257-4.632714.73373.5192
102.7757-0.30790.66973.1130.29523.16140.13250.584-0.21430.1686-0.3338-0.05930.4898-0.03530.04080.21570.03080.01110.2688-0.02080.11826.65231.555511.7778
112.1232-0.1418-2.08274.48942.12068.65620.0107-0.9709-0.090.51730.1816-0.56410.69040.7093-0.13140.19950.0668-0.11410.75060.00830.580827.38624.68568.8303
129.01181.05733.48354.33490.73496.48570.12160.2038-0.33630.45210.11320.19470.4774-0.3847-0.31410.26910.00630.14760.3503-0.01210.2769-5.26845.834635.1079
133.4979-0.6382-0.34384.73180.68944.7443-0.2763-0.3304-0.19330.19960.0418-0.1240.42480.32090.06460.34670.00180.06690.20240.02730.16044.64894.508533.0026
146.07870.99470.01984.98390.18173.4164-0.126-0.05210.362-0.02320.0124-0.0365-0.563-0.06290.14120.279-0.02930.0230.2003-0.05590.13180.997612.128524.6803
152.63750.82181.25972.02381.97982.02340.2150.5259-0.2778-0.17290.3341-0.14230.403-0.0296-0.46390.8068-0.0540.16830.627-0.05270.47580.7152-9.897215.1377
164.7594-0.6444-0.12563.4444-0.11343.5369-0.0786-0.1289-0.18440.0065-0.14260.22110.2168-0.71220.1350.17420.02170.07240.3474-0.06880.1334-2.2534.841618.2126
174.31233.3981-1.80118.5391-2.21363.01610.0523-0.1926-0.6018-0.20090.151-0.810.49810.6669-0.18830.78090.30750.04060.59070.10610.615313.7896-6.093233.1679
188.7911-0.70971.56833.40961.48221.2510.05670.23810.740.0098-0.4485-0.4831-0.77670.880.38260.5395-0.20270.31120.3970.11450.978625.130617.82511.2765
196.29770.74333.70183.5779-0.20324.5468-0.1623-0.8004-1.37160.65150.07240.5761.0653-0.34610.05831.1343-0.01950.27270.3940.16450.72050.0046-13.03835.8171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 321 )A305 - 321
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A322 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 394 )A339 - 394
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 407 )A395 - 407
5X-RAY DIFFRACTION5chain 'A' and (resid 408 through 420 )A408 - 420
6X-RAY DIFFRACTION6chain 'A' and (resid 421 through 438 )A421 - 438
7X-RAY DIFFRACTION7chain 'A' and (resid 439 through 455 )A439 - 455
8X-RAY DIFFRACTION8chain 'A' and (resid 456 through 472 )A456 - 472
9X-RAY DIFFRACTION9chain 'A' and (resid 473 through 496 )A473 - 496
10X-RAY DIFFRACTION10chain 'A' and (resid 497 through 531 )A497 - 531
11X-RAY DIFFRACTION11chain 'A' and (resid 532 through 548 )A532 - 548
12X-RAY DIFFRACTION12chain 'B' and (resid 305 through 338 )B305 - 338
13X-RAY DIFFRACTION13chain 'B' and (resid 339 through 420 )B339 - 420
14X-RAY DIFFRACTION14chain 'B' and (resid 421 through 455 )B421 - 455
15X-RAY DIFFRACTION15chain 'B' and (resid 456 through 465 )B456 - 465
16X-RAY DIFFRACTION16chain 'B' and (resid 466 through 531 )B466 - 531
17X-RAY DIFFRACTION17chain 'B' and (resid 532 through 548 )B532 - 548
18X-RAY DIFFRACTION18chain 'C' and (resid 687 through 696 )C687 - 696
19X-RAY DIFFRACTION19chain 'D' and (resid 688 through 697 )D688 - 697

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