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- PDB-7uj8: Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 7uj8
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with 4-Hydroxytamoxifen
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Alpha helical bundle / hormone receptor / breast cancer / tamoxifen / activating mutation
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / 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 ...regulation of epithelial cell apoptotic process / 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 / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / 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 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / 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 / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / 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 / cytoplasm / cytosol
Similarity search - Function
Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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: 2.385 Å
AuthorsHosfield, D.J. / Greene, G.L. / Fanning, S.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Elife / Year: 2022
Title: Stereospecific lasofoxifene derivatives reveal the interplay between estrogen receptor alpha stability and antagonistic activity in ESR1 mutant breast cancer cells.
Authors: Hosfield, D.J. / Weber, S. / Li, N.S. / Suavage, M. / Joiner, C.F. / Hancock, G.R. / Sullivan, E.A. / Ndukwe, E. / Han, R. / Cush, S. / Laine, M. / Mader, S.C. / Greene, G.L. / Fanning, S.W.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Estrogen receptor
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8434
Polymers60,0682
Non-polymers7752
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-6 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.201, 55.067, 97.479
Angle α, β, γ (deg.)90.000, 113.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 30034.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical ChemComp-OHT / 4-HYDROXYTAMOXIFEN


Mass: 387.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3,350, MgCl2, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 19734 / % possible obs: 96.7 % / Redundancy: 3.1 % / CC1/2: 0.912 / Net I/σ(I): 2.83
Reflection shellResolution: 2.38→2.44 Å / Num. unique obs: 977 / CC1/2: 0.751

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFX

5ufx


Resolution: 2.385→38.997 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 1802 10.03 %
Rwork0.2423 16169 -
obs0.2453 17971 87.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.41 Å2 / Biso mean: 47.5385 Å2 / Biso min: 13.64 Å2
Refinement stepCycle: final / Resolution: 2.385→38.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 58 58 3429
Biso mean--37.81 39.56 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063430
X-RAY DIFFRACTIONf_angle_d0.6944635
X-RAY DIFFRACTIONf_chiral_restr0.038554
X-RAY DIFFRACTIONf_plane_restr0.003569
X-RAY DIFFRACTIONf_dihedral_angle_d13.8061232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3853-2.44980.2986760.298667048
2.4498-2.52190.34121000.289784961
2.5219-2.60330.32861300.2998111680
2.6033-2.69630.3211350.2908128491
2.6963-2.80420.33621530.2829136096
2.8042-2.93180.28231460.2786136498
2.9318-3.08630.33511480.2676138798
3.0863-3.27960.28561640.2583137798
3.2796-3.53270.27571470.2523137398
3.5327-3.88790.27011400.2421117483
3.8879-4.44980.21931470.2032139597
4.4498-5.60360.22711540.2137140198
5.6036-38.9970.2611620.2134141996
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)
18.8612.73550.75741.0634-0.50525.3338-0.3099-0.50633.09220.59570.20220.4473-1.4053-0.23820.12251.0910.20480.10360.3493-0.11030.82462.3448.61426.345
26.29616.7177-3.16622.1189-3.55643.9198-0.4651-0.02150.1826-0.6050.43510.18750.0462-0.5253-0.03860.33790.0908-0.03580.3249-0.00990.4141-14.778-11.18821.661
36.89823.86650.66663.6184-1.49122.83840.16030.3203-0.2505-0.2034-0.2061-0.15450.0399-0.29920.0310.22240.08940.04220.3361-0.07810.2949-9.789-9.80415.43
44.58762.6495-0.16813.0219-2.06952.0088-0.25570.12551.2577-0.0587-0.15090.8727-1.58120.57780.37190.5691-0.0192-0.06060.32190.10910.43094.7724.9412.076
56.07921.4016-1.17874.8282-2.51036.378-0.44230.05740.02910.03670.144-0.01390.19230.36960.25320.23190.0664-0.00970.2259-0.06060.25740.322-7.9915.814
66.9950.9652.99032.62890.51045.5460.1566-1.1083-0.33250.7540.02340.71630.575-0.3397-0.14730.40.06240.13980.71070.30240.5845-10.796-16.7930.234
78.61594.00693.83877.2859-2.22546.8284-0.8237-0.383-2.7769-0.84870.774-1.19680.5798-0.77980.12310.6531-0.03120.21010.6340.04481.35-9.975-28.122.82
85.08153.66082.490210.15784.11928.99950.083-1.1203-1.05360.5707-0.3081-0.41330.7858-0.23280.29990.38430.11110.09430.51590.21290.5274-0.476-19.1830.068
96.56730.91121.57743.65210.40333.675-0.3085-0.69070.93120.20560.2258-0.2531-1.1174-0.38770.04970.44750.1432-0.05060.2961-0.14190.51638.214-0.19727.345
107.58111.88192.99216.28943.15836.6312-0.0514-0.46-0.29490.17410.15750.06540.0630.2295-0.09420.22860.11380.04720.316-0.01650.26898.137-13.26325.345
112.507-1.89231.13812.0479-7.44936.4634-0.18350.2873-0.0746-2.36140.29221.60020.9324-1.0159-0.17180.7272-0.0793-0.12270.9176-0.09490.4526-5.677-8.5624.758
126.30951.0019-2.44196.1811.35278.3892-0.5005-1.43790.66191.27290.4541-0.56630.67140.60380.08030.45690.1316-0.12530.5038-0.040.29230.806-15.93437.375
135.3221-1.1006-0.05266.55441.77293.53630.2085-0.1067-0.9095-0.1924-0.15920.24870.48080.3145-0.04980.27630.0992-0.04260.2768-0.01890.321525.11-27.80121.721
148.0006-2.7514-1.63556.70132.4426.02940.40861.83520.4391-1.0938-0.21820.2859-0.42720.3232-0.14590.55250.13090.05930.6180.11060.360126.555-19.4245.199
158.82085.63827.91239.52949.57422.3991-0.24710.83720.6743-1.437-0.04220.2188-1.29250.06280.34340.51350.02560.0180.61650.14230.337322.363-11.4711.06
165.38571.2891-0.7857.88390.58075.4431-0.1308-0.52420.47620.49750.04530.2391-0.3009-0.18670.08660.26260.115-0.0750.3059-0.02390.243822.314-12.34130.835
175.62912.87443.58379.69755.60617.6436-0.1032-0.15760.2191-0.482-0.54050.8096-0.4078-0.49090.60660.19830.11020.03270.26340.01730.321416.001-12.72920.107
182.23971.4150.00723.95762.90212.7454-0.42020.0991-2.4731-0.0256-0.40.1732.6333-0.38510.36431.38430.19640.52310.260.0431.651419.804-37.65826.114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 309:321 )A309 - 321
2X-RAY DIFFRACTION2( CHAIN A AND RESID 322:334 )A322 - 334
3X-RAY DIFFRACTION3( CHAIN A AND RESID 342:363 )A342 - 363
4X-RAY DIFFRACTION4( CHAIN A AND RESID 364:371 )A364 - 371
5X-RAY DIFFRACTION5( CHAIN A AND RESID 372:394 )A372 - 394
6X-RAY DIFFRACTION6( CHAIN A AND RESID 395:412 )A395 - 412
7X-RAY DIFFRACTION7( CHAIN A AND RESID 413:420 )A413 - 420
8X-RAY DIFFRACTION8( CHAIN A AND RESID 421:437 )A421 - 437
9X-RAY DIFFRACTION9( CHAIN A AND RESID 438:496 )A438 - 496
10X-RAY DIFFRACTION10( CHAIN A AND RESID 497:526 )A497 - 526
11X-RAY DIFFRACTION11( CHAIN A AND RESID 527:545 )A527 - 545
12X-RAY DIFFRACTION12( CHAIN B AND RESID 309:321 )B309 - 321
13X-RAY DIFFRACTION13( CHAIN B AND RESID 322:394 )B322 - 394
14X-RAY DIFFRACTION14( CHAIN B AND RESID 395:423 )B395 - 423
15X-RAY DIFFRACTION15( CHAIN B AND RESID 424:437 )B424 - 437
16X-RAY DIFFRACTION16( CHAIN B AND RESID 438:496 )B438 - 496
17X-RAY DIFFRACTION17( CHAIN B AND RESID 497:526 )B497 - 526
18X-RAY DIFFRACTION18( CHAIN B AND RESID 527:545 )B527 - 545

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