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- PDB-9bqe: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

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Basic information

Entry
Database: PDB / ID: 9bqe
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with (6'-hydroxy-1'-(4-(2-(1-propylpyrrolidin-3-yl)ethoxy)phenyl)-1',4'-dihydro-2'H-spiro[cyclopropane-1,3'-isoquinolin]-2'-yl)(phenyl)methanone
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Estrogen Receptor / Breast Cancer / Alpha Helical Bundle
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 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 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 / negative regulation of miRNA transcription / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / euchromatin / negative regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / transcription regulator complex / Estrogen-dependent gene expression / 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 transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein kinase binding / 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 / 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 ...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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor
Similarity search - Domain/homology
Chem-TV3 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYoung, K.Y. / Fanning, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R37CA279341 United States
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with (6'-hydroxy-1'-(4-(2-(1-propylpyrrolidin-3-yl)ethoxy)phenyl)-1',4'-dihydro-2'H-spiro[cyclopropane-1,3'-isoquinolin]- ...Title: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with (6'-hydroxy-1'-(4-(2-(1-propylpyrrolidin-3-yl)ethoxy)phenyl)-1',4'-dihydro-2'H-spiro[cyclopropane-1,3'-isoquinolin]-2'-yl)(phenyl)methanone
Authors: Fanning, S.W.
History
DepositionMay 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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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)61,0254
Polymers60,0322
Non-polymers9932
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-10 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.177, 56.944, 87.716
Angle α, β, γ (deg.)90.00, 104.53, 90.00
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: 30015.990 Da / Num. of mol.: 2 / Mutation: C381S, C417S, C530S, 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) / References: UniProt: P03372
#2: Chemical ChemComp-TV3 / [(1'R)-6'-hydroxy-1'-(4-{[(3R)-1-propylpyrrolidin-3-yl]methoxy}phenyl)-1',4'-dihydro-2'H-spiro[cyclopropane-1,3'-isoquinolin]-2'-yl](phenyl)methanone


Mass: 496.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H36N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3,350, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 37473 / % possible obs: 99 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Net I/σ(I): 454
Reflection shellResolution: 1.88→1.92 Å / Num. unique obs: 2040 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→40.6 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1181 4.9 %
Rwork0.2175 --
obs0.2199 24115 69.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 74 121 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063548
X-RAY DIFFRACTIONf_angle_d1.0774808
X-RAY DIFFRACTIONf_dihedral_angle_d12.531476
X-RAY DIFFRACTIONf_chiral_restr0.09569
X-RAY DIFFRACTIONf_plane_restr0.008589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.070.3936120.3062160X-RAY DIFFRACTION4
2.07-2.180.2884710.29551362X-RAY DIFFRACTION33
2.18-2.310.4233850.29181560X-RAY DIFFRACTION38
2.31-2.490.32821990.25763987X-RAY DIFFRACTION97
2.49-2.740.3022050.24384106X-RAY DIFFRACTION100
2.74-3.140.27752170.22454116X-RAY DIFFRACTION100
3.14-3.950.27431620.22183500X-RAY DIFFRACTION84
3.96-40.60.21792300.18084143X-RAY DIFFRACTION99
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)
13.28630.87530.71752.26290.94311.47460.10620.18910.495-0.02880.00340.4426-0.2479-0.3176-0.06660.27020.0914-0.00370.2106-0.00480.3207-0.9168-13.875522.7181
23.4411-0.1014-1.19821.0352-0.57173.7305-0.03840.2437-0.09970.14080.0030.0065-0.176-0.4680.02660.18510.0370.00470.1789-0.01330.1681-0.2588-22.813921.2192
32.8184-0.81320.54690.51330.46091.55950.1336-1.2462-1.29620.66210.0116-0.03161.199-0.48990.14370.66840.09330.17560.37230.1240.5586-3.9055-34.163837.628
42.88341.92460.43114.902-0.31673.77380.1729-0.1728-0.49740.9013-0.0207-0.12530.1824-0.0880.05240.350.0362-0.00450.20540.03590.25047.2267-27.585335.5062
52.48630.6832-0.09591.9025-0.12133.7368-0.02070.150.05540.11250.0714-0.2467-0.25340.26610.03660.19630.0063-0.01130.12330.03440.214.2132-15.518517.3981
62.2280.4524-1.66873.5995-0.69812.19860.0168-0.1806-0.17180.0101-0.218100.150.07080.19420.19370.0959-0.00750.23150.02970.214313.6663-25.435526.6303
72.6273-1.01650.31753.6953-1.09974.11590.61390.885-0.23070.3442-0.54291.020.0319-1.1955-0.36080.3073-0.13810.03181.0704-0.2490.5409-5.3205-24.01746.8936
80.7999-1.69391.22835.2365-1.53776.3433-0.0680.9806-0.17580.8458-0.0238-1.1451-1.1799-0.0650.41380.2869-0.1075-0.08430.34230.01220.645239.9787-24.018430.3888
92.7539-1.2705-1.66135.42010.53083.1589-0.3864-0.2666-0.0797-0.1410.14350.18060.3180.16180.20520.21080.1214-0.02370.3116-0.01040.283832.9714-44.293223.0276
101.9269-0.93320.11213.59990.75841.7867-0.03130.07460.27220.37950.0503-0.1240.01420.1757-0.02650.22380.08690.01540.30690.00680.21127.5209-35.854327.0401
111.6573-1.45122.02571.4248-1.56994.12061.09470.8341-0.6609-1.1352-0.85830.29840.69980.27690.39170.40280.256-0.05840.5193-0.06920.277727.9264-44.00097.8121
125.18641.33710.84895.83331.33063.1887-0.40440.9345-0.1858-0.77190.60090.1931-0.27010.1544-0.12250.29030.0577-0.04470.41260.02770.227622.7111-33.109510.3461
131.7325-0.51730.71923.734602.9106-0.0963-0.06950.4090.25780.0606-0.3844-0.09730.61330.0780.16920.0241-0.06820.33230.03810.40928.7414-22.891428.4995
142.91352.31950.08974.82960.73371.3892-0.07110.0639-0.0999-0.5651-0.2231-0.3911-0.09860.10020.05450.19750.0556-0.00360.30820.05280.182620.6753-26.093319.5633
150.782-0.18690.38340.8915-0.68487.7268-0.3902-1.0292-0.42270.45840.3092-0.1990.63090.56270.0661.01990.10060.1540.29570.25190.339826.7571-47.386335.2223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 306 through 341 )
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 407 )
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 420 )
4X-RAY DIFFRACTION4chain 'A' and (resid 421 through 438 )
5X-RAY DIFFRACTION5chain 'A' and (resid 439 through 496 )
6X-RAY DIFFRACTION6chain 'A' and (resid 497 through 526 )
7X-RAY DIFFRACTION7chain 'A' and (resid 527 through 549 )
8X-RAY DIFFRACTION8chain 'B' and (resid 309 through 322 )
9X-RAY DIFFRACTION9chain 'B' and (resid 323 through 363 )
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 400 )
11X-RAY DIFFRACTION11chain 'B' and (resid 401 through 420 )
12X-RAY DIFFRACTION12chain 'B' and (resid 421 through 438 )
13X-RAY DIFFRACTION13chain 'B' and (resid 439 through 496 )
14X-RAY DIFFRACTION14chain 'B' and (resid 497 through 524 )
15X-RAY DIFFRACTION15chain 'B' and (resid 525 through 546 )

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