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- PDB-5w9c: Estrogen Receptor Alpha Ligand Binding Domain C381S, C417S, C530S... -

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Basic information

Entry
Database: PDB / ID: 5w9c
TitleEstrogen Receptor Alpha Ligand Binding Domain C381S, C417S, C530S in Complex with 4-hydroxytamoxifen
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Breast Cancer / Selective Estrogen Receptor Modulator
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 / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / 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 / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / 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 / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / calmodulin binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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
4-HYDROXYTAMOXIFEN / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsFanning, S.W. / Greene, G.W.
CitationJournal: Mol. Pharmacol. / Year: 2018
Title: Endoxifen, 4-Hydroxytamoxifen and an Estrogenic Derivative Modulate Estrogen Receptor Complex Mediated Apoptosis in Breast Cancer.
Authors: Maximov, P.Y. / Abderrahman, B. / Fanning, S.W. / Sengupta, S. / Fan, P. / Curpan, R.F. / Rincon, D.M.Q. / Greenland, J.A. / Rajan, S.S. / Greene, G.L. / Jordan, V.C.
History
DepositionJun 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0438
Polymers113,4934
Non-polymers1,5504
Water6,954386
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5224
Polymers56,7462
Non-polymers7752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-13 kcal/mol
Surface area19950 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5224
Polymers56,7462
Non-polymers7752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-13 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.308, 58.308, 276.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 28373.242 Da / Num. of mol.: 4 / Mutation: C381S, C417S, C530S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03372
#2: Chemical
ChemComp-OHT / 4-HYDROXYTAMOXIFEN


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


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 56362 / % possible obs: 60.3 % / Redundancy: 1.6 % / Net I/σ(I): 0.024
Reflection shellResolution: 1.8→1.83 Å / % possible all: 52.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACC

5acc


Resolution: 1.802→19.628 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.242 2730 4.84 %
Rwork0.1968 --
obs0.199 56362 57.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.802→19.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7164 0 116 386 7666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047435
X-RAY DIFFRACTIONf_angle_d0.73910057
X-RAY DIFFRACTIONf_dihedral_angle_d13.9292689
X-RAY DIFFRACTIONf_chiral_restr0.0311199
X-RAY DIFFRACTIONf_plane_restr0.0031235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8022-1.83330.3156550.25731242X-RAY DIFFRACTION26
1.8333-1.86660.318750.25471608X-RAY DIFFRACTION35
1.8666-1.90250.2721960.2491982X-RAY DIFFRACTION43
1.9025-1.94130.33241140.23922275X-RAY DIFFRACTION48
1.9413-1.98340.27911160.24522331X-RAY DIFFRACTION51
1.9834-2.02950.31441230.22742253X-RAY DIFFRACTION49
2.0295-2.08020.30171050.22862281X-RAY DIFFRACTION48
2.0802-2.13640.28171270.20752244X-RAY DIFFRACTION49
2.1364-2.19920.24551150.20932327X-RAY DIFFRACTION50
2.1992-2.27010.241270.20262379X-RAY DIFFRACTION52
2.2701-2.35110.23771460.20612507X-RAY DIFFRACTION54
2.3511-2.44510.28471430.20212734X-RAY DIFFRACTION59
2.4451-2.55610.23951540.20092957X-RAY DIFFRACTION64
2.5561-2.69060.23871730.20873087X-RAY DIFFRACTION68
2.6906-2.85870.25951640.21133339X-RAY DIFFRACTION72
2.8587-3.07860.22161810.19673494X-RAY DIFFRACTION75
3.0786-3.3870.23161740.19823575X-RAY DIFFRACTION78
3.387-3.87380.22541720.1743705X-RAY DIFFRACTION79
3.8738-4.86830.20581970.16263710X-RAY DIFFRACTION81
4.8683-19.62950.23971730.19773602X-RAY DIFFRACTION78
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)
12.9231-1.80640.95315.1058-0.2681.5427-0.4112-0.39140.82930.74980.1722-0.978-0.5342-0.07570.11110.2779-0.1613-0.09440.1547-0.09360.468518.42716.3768-18.8908
23.30040.07290.12612.9468-0.94452.76130.14640.6753-0.2706-0.6763-0.3191-0.05660.57960.06950.15490.09120.00590.05450.3202-0.00060.243126.1533-8.7078-33.2209
33.1806-1.2697-0.93473.53560.52582.8112-0.245-0.4255-0.37290.0988-0.3959-0.05060.52530.22570.1509-0.0107-0.0027-0.02690.17780.0040.162620.9376-7.3602-23.8351
42.1278-0.584-0.10861.11920.12035.1513-0.0245-0.12630.0170.06290.0319-0.0103-0.01180.1558-0.02650.06680.0051-0.02170.1204-0.01230.096312.8928-0.7699-18.2013
52.633-0.38451.96271.73760.06162.4003-0.2129-0.12110.2393-0.37690.167-0.2562-0.35560.3963-0.24390.1353-0.00390.08270.48160.06440.148118.8198-2.0126-39.3572
63.3337-0.61850.23812.51930.13012.44-0.15760.569-0.8099-0.4673-0.22370.58590.6106-0.17260.27930.32090.01250.02240.4023-0.10020.350914.2707-12.3256-41.5946
73.670.4959-0.58156.7134-0.07875.4340.07630.36850.0783-0.681-0.4202-0.04880.00820.22450.19430.1360.0404-0.00190.26190.02280.07977.9992-1.066-38.4827
82.4751-0.3904-0.36383.03150.61524.4262-0.0361-0.08940.17410.0490.0423-0.0295-0.1021-0.0098-0.09550.1052-0.013-0.020.10110.00420.15388.72495.8788-21.7862
91.9807-0.6801-0.07552.6069-0.15041.8338-0.0972-0.25660.35410.04020.09970.0271-0.27490.250.02270.2346-0.0533-0.05880.109-0.05870.17346.782313.9141-16.6021
102.3193-1.29290.26356.926-0.94281.3925-0.07810.0606-0.08-0.00370.0299-0.1823-0.0456-0.02310.01240.0847-0.02260.00150.14430.01730.05963.77421.1001-28.5448
112.47030.80750.70073.81232.15512.3649-0.3603-0.7031-0.93770.57660.9062-0.23670.61710.8562-0.14050.62880.3185-0.13360.5699-0.00930.060117.2558-11.815-12.481
122.0522.0461-0.58315.4061-0.84362.4067-0.12150.16240.38060.1270.24550.3694-0.1783-0.6037-0.15920.12030.0996-0.0010.2844-0.03920.2251-23.07262.2647-24.5042
133.00980.9756-0.28751.6162-0.0392.3391-0.0707-0.0347-0.0397-0.016-0.04460.0884-0.0916-0.42220.06540.06280.0006-0.00730.1193-0.00160.1195-16.6348-3.0854-27.3459
145.86463.2171-0.57684.6499-0.32331.96550.3093-0.7933-0.75160.6897-0.6468-0.51370.03010.04270.16820.1931-0.01270.02640.38630.05740.13-10.353-5.4335-11.688
151.59481.08380.38742.9356-0.45253.3011-0.07380.23020.2985-0.11020.05090.0995-0.1662-0.01770.04450.12380.048-0.03780.14150.04460.1898-7.615910.2791-32.3158
162.3966-0.13830.04531.3617-1.52262.862-0.24870.1342-0.2731-0.52760.4092-0.15910.3024-0.1919-0.09740.1169-0.02550.00460.1815-0.02090.0716-7.4489-2.994-26.8991
172.20410.8775-1.18433.914-0.28631.375-0.0846-0.0879-0.21740.01890.0737-0.19620.29460.35140.05050.13490.0890.01970.14310.01140.16829.301814.231721.2761
180.5955-0.0159-0.04822.0424-0.00182.7108-0.00230.1282-0.0659-0.3122-0.05190.03850.10340.18760.06560.21340.05920.00440.1233-0.00020.13054.240121.097116.5206
191.68590.79070.45312.5677-0.43753.3860.0084-0.06740.00410.1609-0.0463-0.3452-0.02150.24090.00310.09630.0026-0.03570.14380.02230.148512.932932.127326.8733
201.5132-0.16030.55832.5730.66492.51410.3056-0.1248-0.07180.511-0.18870.25810.3147-0.0313-0.04520.18870.0324-0.01940.12910.00370.07971.291324.63623.2532
213.4931-0.25920.51141.39561.10471.54440.066-0.11290.1471-0.0584-0.1712-0.0228-0.5554-0.19820.04720.23820.0294-0.03520.12440.02910.14-12.774552.021720.4369
222.1932-1.0221-0.56821.61590.58365.1191-0.1689-0.19940.02910.24720.0340.0947-0.1392-0.10580.12620.1140.0202-0.01140.0747-0.00440.1167-8.990643.26225.5177
232.85280.6156-0.17161.7467-0.37932.37240.01260.05320.1971-0.2696-0.0898-0.2623-0.54460.10310.01450.1759-0.02940.02710.09090.05150.17875.381746.060814.4182
242.0382-0.4834-1.08241.9248-0.79272.4348-0.0420.6187-0.3151-0.02890.06940.0652-0.1813-0.2430.03310.15370.05070.01230.1307-0.02320.0899-5.079938.596519.8687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 309 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 339 )
3X-RAY DIFFRACTION3chain 'A' and (resid 340 through 363 )
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 394 )
5X-RAY DIFFRACTION5chain 'A' and (resid 395 through 407 )
6X-RAY DIFFRACTION6chain 'A' and (resid 408 through 421 )
7X-RAY DIFFRACTION7chain 'A' and (resid 422 through 437 )
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 465 )
9X-RAY DIFFRACTION9chain 'A' and (resid 466 through 496 )
10X-RAY DIFFRACTION10chain 'A' and (resid 497 through 528 )
11X-RAY DIFFRACTION11chain 'A' and (resid 529 through 547 )
12X-RAY DIFFRACTION12chain 'B' and (resid 307 through 341 )
13X-RAY DIFFRACTION13chain 'B' and (resid 342 through 407 )
14X-RAY DIFFRACTION14chain 'B' and (resid 408 through 438 )
15X-RAY DIFFRACTION15chain 'B' and (resid 439 through 496 )
16X-RAY DIFFRACTION16chain 'B' and (resid 497 through 545 )
17X-RAY DIFFRACTION17chain 'C' and (resid 309 through 363 )
18X-RAY DIFFRACTION18chain 'C' and (resid 364 through 437 )
19X-RAY DIFFRACTION19chain 'C' and (resid 438 through 496 )
20X-RAY DIFFRACTION20chain 'C' and (resid 497 through 547 )
21X-RAY DIFFRACTION21chain 'D' and (resid 308 through 363 )
22X-RAY DIFFRACTION22chain 'D' and (resid 364 through 438 )
23X-RAY DIFFRACTION23chain 'D' and (resid 439 through 496 )
24X-RAY DIFFRACTION24chain 'D' and (resid 497 through 544 )

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