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- PDB-7rs1: Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L... -

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Basic information

Entry
Database: PDB / ID: 7rs1
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with DMERI-21
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / ER-alpha / ligand complex / DMERI / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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 / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / 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 / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / 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 / 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
Chem-7Q5 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.59 Å
AuthorsMin, J. / Nwachukwu, J.C. / Min, C.K. / Njeri, J.W. / Srinivasan, S. / Rangarajan, E.S. / Nettles, C.C. / Yan, S. / Houtman, R. / Griffin, P.R. ...Min, J. / Nwachukwu, J.C. / Min, C.K. / Njeri, J.W. / Srinivasan, S. / Rangarajan, E.S. / Nettles, C.C. / Yan, S. / Houtman, R. / Griffin, P.R. / Izard, T. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Nettles, K.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Dual-mechanism estrogen receptor inhibitors.
Authors: Min, J. / Nwachukwu, J.C. / Min, C.K. / Njeri, J.W. / Srinivasan, S. / Rangarajan, E.S. / Nettles, C.C. / Sanabria Guillen, V. / Ziegler, Y. / Yan, S. / Carlson, K.E. / Hou, Y. / Kim, S.H. / ...Authors: Min, J. / Nwachukwu, J.C. / Min, C.K. / Njeri, J.W. / Srinivasan, S. / Rangarajan, E.S. / Nettles, C.C. / Sanabria Guillen, V. / Ziegler, Y. / Yan, S. / Carlson, K.E. / Hou, Y. / Kim, S.H. / Novick, S. / Pascal, B.D. / Houtman, R. / Griffin, P.R. / Izard, T. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionAug 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
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

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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)119,9288
Polymers117,5224
Non-polymers2,4064
Water8,683482
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9644
Polymers58,7612
Non-polymers1,2032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area18820 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9644
Polymers58,7612
Non-polymers1,2032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-13 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.580, 58.768, 93.153
Angle α, β, γ (deg.)86.710, 75.090, 62.870
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 29380.520 Da / Num. of mol.: 4 / Fragment: Ligand binding domain / Mutation: L372S, L536S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372
#2: Chemical
ChemComp-7Q5 / methyl 3-(4-{[(1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonyl](2,2,2-trifluoroethyl)amino}phenyl)prop-2-enoate


Mass: 601.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H26F3NO7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 42.56 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 20-25% PEG 3350, 200 mM MgCl2, 0.1 M Bis-Tris/Hepes/Tris-HCl
PH range: 6.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→89.9 Å / Num. obs: 93507 / % possible obs: 91.4 % / Redundancy: 7.9 % / CC1/2: 0.999 / Net I/σ(I): 17.1
Reflection shellResolution: 1.59→1.73 Å / Num. unique obs: 4676 / CC1/2: 0.486

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
AutoProcessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2QXS

2qxs


Resolution: 1.59→89.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.802 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 4613 4.9 %RANDOM
Rwork0.1859 ---
obs0.1876 88898 71.04 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 128.08 Å2 / Biso mean: 34.887 Å2 / Biso min: 12.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å2-0.57 Å2-0.21 Å2
2--0.44 Å2-0.11 Å2
3----2.1 Å2
Refinement stepCycle: final / Resolution: 1.59→89.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7265 0 160 482 7907
Biso mean--46.07 39.23 -
Num. residues----912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0187584
X-RAY DIFFRACTIONr_bond_other_d0.0010.027241
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.93910266
X-RAY DIFFRACTIONr_angle_other_deg1.1972.93416770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8245901
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27124.387310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.175151407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8831538
X-RAY DIFFRACTIONr_chiral_restr0.0940.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021435
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.629 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.361 5 -
Rwork0.399 203 -
obs--2.13 %
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)
11.4632-0.63520.3092.9943-0.70841.3298-0.0210.06320.0699-0.0921-0.00320.0501-0.06960.00280.02410.0197-0.00380.02920.0234-0.03260.17836.092.10924.006
21.93410.34250.19451.7679-0.00231.2883-0.01550.06270.0656-0.02710.0540.16550.0881-0.1726-0.03860.0394-0.00180.05850.03790.01820.1952-6.085-19.64625.733
31.52030.5148-0.29833.7319-1.30981.9210.0319-0.0121-0.0789-0.0537-0.0448-0.02870.22580.14870.0130.07420.06140.03730.1001-0.03890.175430.143-9.65669.447
41.5103-0.21640.322.16780.05882.5102-0.0657-0.13360.01530.12020.08560.0954-0.1868-0.2077-0.01990.04580.0430.05380.05660.01470.169317.67511.76767.701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 546
2X-RAY DIFFRACTION2B303 - 546
3X-RAY DIFFRACTION3C305 - 546
4X-RAY DIFFRACTION4D305 - 546

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