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- PDB-7kbs: Estrogen Receptor Alpha Ligand Binding Domain in Complex with Ral... -

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Basic information

Entry
Database: PDB / ID: 7kbs
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with Raloxifene
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Estrogen Receptor / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / 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 / 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 / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / 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 / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...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 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
Similarity search - Domain/homology
RALOXIFENE / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.834 Å
AuthorsFanning, S.W.
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
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 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
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2894
Polymers60,3422
Non-polymers9472
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-13 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.802, 57.879, 87.950
Angle α, β, γ (deg.)90.000, 102.930, 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: 30171.119 Da / Num. of mol.: 2 / Fragment: Alpha Ligand Binding Domain, residues 307-554 / Mutation: L536S, C381S, C417S, C530S
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-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8,000, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.834→30.864 Å / Num. obs: 39139 / % possible obs: 89.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.01
Reflection shellResolution: 1.834→1.9 Å / Num. unique obs: 7108 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFX

5ufx


Resolution: 1.834→30.864 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 2030 5.19 %
Rwork0.1713 37109 -
obs0.1732 39139 89.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.99 Å2 / Biso mean: 23.226 Å2 / Biso min: 3.72 Å2
Refinement stepCycle: final / Resolution: 1.834→30.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 68 338 4150
Biso mean--18.45 31.66 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073926
X-RAY DIFFRACTIONf_angle_d1.0055321
X-RAY DIFFRACTIONf_chiral_restr0.041618
X-RAY DIFFRACTIONf_plane_restr0.004659
X-RAY DIFFRACTIONf_dihedral_angle_d14.2141447
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.834-1.87660.3122780.2167136350
1.8766-1.92350.2603950.2092178165
1.9235-1.97550.22371270.2004207576
1.9755-2.03360.25031510.1911229583
2.0336-2.09930.2261120.1879248489
2.0993-2.17430.2341370.1683257493
2.1743-2.26130.21361480.1623259094
2.2613-2.36420.17321370.163265396
2.3642-2.48880.21951580.169271599
2.4888-2.64460.21761470.1647279199
2.6446-2.84870.20651590.1707273799
2.8487-3.13510.20021660.15892755100
3.1351-3.58820.21341550.1575276399
3.5882-4.51840.16131350.1527277298
4.5184-30.8640.23661250.197276195
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)
11.85260.85-0.51111.6474-0.16711.4271-0.02430.14290.04390.0994-0.0035-0.0332-0.1265-0.18110.0750.14410.0444-0.02470.12250.01260.184-2.6057-15.148424.5315
22.09370.9104-0.69831.5801-0.32621.47180.00180.134-0.0441-0.0094-0.06890.0641-0.0065-0.11340.01180.10790.0458-0.01310.1282-0.00680.1267-5.8444-25.172321.5447
31.41060.3239-0.17310.6131-0.34341.61-0.0108-0.0006-0.02390.0440.0145-0.0254-0.0179-0.0728-0.01650.09780.02930.00340.0698-0.00370.09544.5285-24.146727.0364
40.04540.0203-0.337-0.0222-0.03591.36030.01240.1772-0.2485-0.5362-0.16930.10530.4740.12010.07850.50120.04660.13040.40740.16360.475714.9065-27.96117.0261
51.40360.67060.69281.97791.41484.5515-0.01280.21780.1855-0.12320.0423-0.1358-0.1339-0.0062-0.00770.1460.0114-0.00080.15650.04090.159417.5148-12.915614.9897
61.92731.24460.31412.44420.22630.843-0.0153-0.0024-0.0490.0172-0.0168-0.04240.04340.08420.03030.09590.03140.01620.1027-0.00430.114813.6447-26.211426.6289
70.68360.2551-0.07372.0464-1.22672.0066-0.04770.3471-0.0494-0.61690.16210.47570.1575-0.16960.03660.2999-0.0513-0.05090.49620.02690.2265-5.3463-27.3988.4863
81.29370.08280.07811.858-0.0811.3059-0.01540.1389-0.0498-0.00420.0318-0.24440.14230.11970.08090.08940.01960.00860.17530.02610.152337.586-3822.8405
91.0370.27030.20072.61571.10121.90710.01330.006-0.1591-0.1775-0.0633-0.05480.00080.02490.01270.11390.0540.01670.13020.00390.140831.5347-44.96724.81
100.706-0.30270.01570.76630.22731.66150.0105-0.0283-0.01170.0495-0.02740.0088-0.0319-0.02470.00990.10330.0265-0.00150.10450.01360.10526.9561-36.27830.4899
111.3142-0.92970.18142.0987-1.19841.662-0.18210.45290.1889-0.78340.0358-0.2824-0.26430.392-0.00670.26360.16020.09950.29220.0460.119632.5473-39.00169.2008
121.6382-0.53020.24520.17090.02050.29810.03120.4668-0.3877-0.4357-0.16290.32580.2141-0.27090.07970.32810.1126-0.03750.4662-0.12470.251722.4067-46.17336.7804
132.32661.3650.25964.06480.43991.79180.11610.3572-0.0346-0.6428-0.23040.2311-0.2886-0.2729-0.00030.26230.1696-0.03750.39950.01710.058323.1407-33.1779.9744
141.1854-0.02060.23491.8778-0.02972.0030.14080.04780.08250.14810.00290.0801-0.2216-0.2502-0.06250.11380.04430.02480.11950.02460.159727.3883-27.875426.7341
151.48280.1252-0.55652.3323-1.15882.9291-0.0397-0.13820.14580.30210.06710.0165-0.00960.06760.00880.15330.006-0.03170.1347-0.01650.191229.2452-20.352632.3197
161.10681.04160.13743.6753-0.07370.48490.03280.09460.0292-0.1057-0.04370.1115-0.0013-0.0333-0.00740.10950.03310.0020.13150.00460.138320.7383-27.721819.6973
170.14940.26430.26470.36080.41110.38150.16870.1992-0.9222-0.40260.02870.52830.6269-0.1146-0.10910.3536-0.0003-0.09180.2548-0.04720.339618.7053-50.969326.0158
183.19181.59940.57353.95920.83573.7955-0.0604-0.2513-0.2828-0.0856-0.253-0.32980.27680.5826-0.00510.22680.01310.01950.20330.06630.109828.876-46.167338.7116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 338 )A307 - 338
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 363 )A339 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 455 )A364 - 455
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 465 )A456 - 465
5X-RAY DIFFRACTION5chain 'A' and (resid 466 through 496 )A466 - 496
6X-RAY DIFFRACTION6chain 'A' and (resid 497 through 528 )A497 - 528
7X-RAY DIFFRACTION7chain 'A' and (resid 529 through 550 )A529 - 550
8X-RAY DIFFRACTION8chain 'B' and (resid 306 through 341 )B306 - 341
9X-RAY DIFFRACTION9chain 'B' and (resid 342 through 363 )B342 - 363
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 394 )B364 - 394
11X-RAY DIFFRACTION11chain 'B' and (resid 395 through 407 )B395 - 407
12X-RAY DIFFRACTION12chain 'B' and (resid 408 through 421 )B408 - 421
13X-RAY DIFFRACTION13chain 'B' and (resid 422 through 437 )B422 - 437
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 466 )B438 - 466
15X-RAY DIFFRACTION15chain 'B' and (resid 467 through 496 )B467 - 496
16X-RAY DIFFRACTION16chain 'B' and (resid 497 through 527 )B497 - 527
17X-RAY DIFFRACTION17chain 'B' and (resid 528 through 536 )B528 - 536
18X-RAY DIFFRACTION18chain 'B' and (resid 537 through 546 )B537 - 546

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