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

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Basic information

Entry
Database: PDB / ID: 5tlo
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with a Squaric Acid-linked Dimeric Estrogen
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Mitochondrial unfolded protein response (UPRmt) / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / : / steroid binding / positive regulation of adipose tissue development / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / 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 / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to estrogen / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / 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) / 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 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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
Chem-7EE / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / 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 11, 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)62,5346
Polymers61,7594
Non-polymers7752
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-30 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.242, 82.284, 58.447
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 / 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


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*PLUS
#3: Chemical ChemComp-7EE / (14beta,17alpha)-21-(4-aminophenyl)-19-norpregna-1(10),2,4-trien-20-yne-3,17-diol


Mass: 387.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.01 Å3/Da / Density % sol: 38.87 % / Mosaicity: 1.082 °
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: NSLS / Beamline: X12C / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: Channel-cut Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.282→50 Å / Num. obs: 22128 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.58 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.348 / % possible all: 99.8

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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: 2.28→46.69 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.87
RfactorNum. reflection% reflection
Rfree0.241 1906 9.08 %
Rwork0.197 --
obs0.201 21002 94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 68.09 Å2
Refinement stepCycle: LAST / Resolution: 2.28→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 50 64 3826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023836
X-RAY DIFFRACTIONf_angle_d0.6185206
X-RAY DIFFRACTIONf_dihedral_angle_d15.0931378
X-RAY DIFFRACTIONf_chiral_restr0.038632
X-RAY DIFFRACTIONf_plane_restr0.002636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2822-2.33920.27141230.22741101X-RAY DIFFRACTION76
2.3392-2.40250.30741270.23681280X-RAY DIFFRACTION88
2.4025-2.47320.34381310.2381276X-RAY DIFFRACTION90
2.4732-2.5530.29821210.23581342X-RAY DIFFRACTION92
2.553-2.64420.30471370.23441316X-RAY DIFFRACTION91
2.6442-2.75010.28021360.22951366X-RAY DIFFRACTION94
2.7501-2.87520.31260.23471366X-RAY DIFFRACTION96
2.8752-3.02680.2671450.21211396X-RAY DIFFRACTION97
3.0268-3.21640.28511420.21881445X-RAY DIFFRACTION99
3.2164-3.46470.24541360.20761441X-RAY DIFFRACTION98
3.4647-3.81320.26521480.19981413X-RAY DIFFRACTION98
3.8132-4.36460.22571410.16751432X-RAY DIFFRACTION98
4.3646-5.49760.19411470.17221478X-RAY DIFFRACTION100
5.4976-46.69640.1991460.18431444X-RAY DIFFRACTION97
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)
17.59160.53084.99278.67930.5737.88750.1584-0.4093-0.0081-0.0279-0.06671.20961.1252-2.1398-0.20550.562-0.21950.11131.0101-0.03620.61-34.510116.6399-1.7106
28.63894.11294.82488.60873.54616.4521-0.52760.006-0.27070.27060.4153-0.8115-0.20641.41810.2050.6320.01090.06990.8648-0.05160.4346-10.97923.517415.8496
35.5460.3461.06226.5641.8938.7347-0.4235-0.4468-0.35270.72480.2223-0.04491.25350.46360.09980.66080.09340.08840.52530.02920.3582-12.167915.73639.9683
43.8313-0.8407-0.55725.26960.91796.6150.10370.0294-0.66070.1461-0.41580.0431.4209-0.25980.27930.7354-0.08870.15070.4514-0.04530.3277-17.296712.0011-0.4856
51.8543-0.79960.12646.69560.91427.2566-0.63420.2876-0.27570.11730.4603-0.5903-1.2234-0.8604-0.1920.5776-0.04870.07440.6162-0.0560.393-12.45232.14136.3536
64.8926-0.518-2.16687.36361.44789.27610.4693-1.1713-0.00430.61210.4607-0.8525-0.74231.1377-0.4830.6061-0.136600.7881-0.21890.474-4.210930.92829.1369
74.0633-2.73463.54556.7111-0.94673.6669-0.14221.13491.03910.5533-0.2582-0.7194-0.9010.84790.32190.7969-0.20110.16370.6091-0.03750.4983-8.719230.709-2.4492
86.46481.1020.02738.6187-1.2177.4871-0.13560.56990.1464-0.0820.1308-0.04190.0769-1.0522-0.07170.41010.01860.14550.4982-0.01430.3308-22.708622.9877-3.8651
94.24211.36752.73047.46512.78944.87040.82950.58250.3536-1.3190.4854-0.9161-0.6309-0.0502-1.38011.374-0.06720.410.9113-0.08110.7461-18.0863.6291-12.4228
105.8042-3.3375-2.38412.9333-1.00667.63670.15490.1701-0.222-1.0575-0.56560.73930.3328-1.38530.46110.4727-0.09470.00060.8479-0.13740.4571-29.805820.3319-11.0507
114.8376-4.08070.17646.3933-2.88047.4535-0.38480.010.3850.04490.0377-0.5063-0.79530.32550.22460.5222-0.03180.11220.3691-0.03150.3781-12.120722.4337-8.0001
123.00241.48223.09426.71782.25543.2439-0.37580.5225-0.26390.54310.46430.30381.60511.9377-0.04611.11580.29820.09140.95510.13390.7741-3.28118.3786.1169
136.67440.3659-0.42636.16950.37751.8377-0.01441.06151.64-0.3998-0.30540.6658-1.2855-0.9373-0.24161.14260.55070.03130.77870.2630.5873-16.606132.9772-32.8066
144.84910.2652-0.51424.7647-0.63777.21430.08240.3424-1.1906-0.1325-0.1430.06880.85690.54050.05990.70450.14110.12190.68740.01650.47873.31699.0648-34.3701
156.2395-1.5464-1.48879.1735-0.76657.84330.0860.1325-0.4587-0.05410.07620.10670.30010.8912-0.0980.49070.02390.12750.4404-0.04450.36063.452517.5064-28.6182
165.98661.0734-0.46154.6494-0.73554.95560.3712-0.34550.88590.4692-0.182-0.0214-0.69960.0634-0.1190.47820.03160.17650.3825-0.02840.4178-3.773926.0288-22.9853
174.02644.0781-3.0896.16340.3749.25030.30220.406-1.12740.219-0.391-0.22531.2964-0.17120.3250.7212-0.03570.14770.4086-0.08570.481-5.94744.8916-30.5606
184.6531.48550.65965.63531.76326.9796-1.4188-0.7788-1.50790.62810.807-1.0461.22430.71620.40321.6530.32480.11090.61150.15211.34892.1118-1.0168-19.8112
193.6523-3.27885.4478.867-2.5849.48280.2655-0.2312-0.8652-0.6317-0.1086-0.00741.4962-0.1330.05710.77350.00720.2020.47590.04910.4536-11.19616.8762-20.8401
207.357-0.0761-1.11724.42351.26965.36110.18380.11930.6145-0.3397-0.210.2341-0.9663-0.84550.0480.6150.21120.08440.49440.07010.351-17.381926.4453-23.6265
212.23090.4505-1.13541.7798-0.32954.72050.2861-0.695-0.69320.0655-0.2153-0.09070.50640.204-0.12380.64060.020.04180.4192-0.02630.3508-6.82915.6527-16.741
222.8954-2.9742-2.80569.09582.5242.7701-0.5534-0.95180.932-0.06580.5686-0.9925-0.48411.5417-0.0870.5115-0.00190.08970.8659-0.08050.74638.607122.623-17.9974
235.9425-3.52311.256.22014.06525.8529-0.7879-1.3144-2.63921.7085-0.22780.22490.9516-0.6790.89211.4413-0.08690.27750.46650.23110.8429-16.71251.53757.9039
244.8848-4.7587-2.15764.77042.13062.56571.1084-0.5852.58530.3778-0.543-1.2503-1.34530.8647-0.58680.778-0.14590.29580.6575-0.13011.19277.926232.1822-26.8044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 306 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 405 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 406 THROUGH 420 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 421 THROUGH 437 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 438 THROUGH 455 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 456 THROUGH 472 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 473 THROUGH 496 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 497 THROUGH 529 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 532 THROUGH 548 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 305 THROUGH 321 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 322 THROUGH 338 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 339 THROUGH 363 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 364 THROUGH 394 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 395 THROUGH 411 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 412 THROUGH 420 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 421 THROUGH 438 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 439 THROUGH 496 )
21X-RAY DIFFRACTION21CHAIN 'B' AND (RESID 497 THROUGH 537 )
22X-RAY DIFFRACTION22CHAIN 'B' AND (RESID 538 THROUGH 548 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 688 THROUGH 696 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 688 THROUGH 696 )

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