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- PDB-7rs7: Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L... -

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Basic information

Entry
Database: PDB / ID: 7rs7
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with DMERI-30
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION/TRANSCRIPTION Inhibitor / ER-alpha / ligand complex / DMERI / TRANSCRIPTION / TRANSCRIPTION-TRANSCRIPTION Inhibitor complex
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 / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / 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 / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related 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
Similarity search - Domain/homology
Chem-73I / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)119,8848
Polymers117,7504
Non-polymers2,1344
Water6,251347
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9424
Polymers58,8752
Non-polymers1,0672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-17 kcal/mol
Surface area20560 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9424
Polymers58,8752
Non-polymers1,0672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-17 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.665, 58.621, 93.932
Angle α, β, γ (deg.)87.270, 74.870, 62.910
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA305 - 5468 - 249
21ALAALABB305 - 5468 - 249
12PROPROAA305 - 5528 - 255
22PROPROCC305 - 5528 - 255
13ASPASPAA305 - 5458 - 248
23ASPASPDD305 - 5458 - 248
14ALAALABB305 - 5468 - 249
24ALAALACC305 - 5468 - 249
15ALAALABB305 - 5468 - 249
25ALAALADD305 - 5468 - 249
16ASPASPCC305 - 5458 - 248
26ASPASPDD305 - 5458 - 248

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 29437.570 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-73I / (1S,2R,4S,5S,6S)-N,5,6-tris(4-hydroxyphenyl)-N-(2,2,2-trifluoroethyl)-7-oxabicyclo[2.2.1]heptane-2-sulfonamide


Mass: 533.516 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H22F3NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
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: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→90.37 Å / Num. obs: 89258 / % possible obs: 86.7 % / Redundancy: 7.3 % / CC1/2: 0.987 / Net I/σ(I): 4
Reflection shellResolution: 1.58→1.639 Å / Num. unique obs: 3316 / CC1/2: 0.475

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Processing

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

2qxs


Resolution: 1.58→90.37 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.788 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4633 4.9 %RANDOM
Rwork0.2232 ---
obs0.2246 89258 70.12 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 212.84 Å2 / Biso mean: 27.969 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.09 Å2-0.02 Å2
2--0.08 Å20.08 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.58→90.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7626 0 182 347 8155
Biso mean--53.35 32.61 -
Num. residues----955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137993
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177581
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.66110839
X-RAY DIFFRACTIONr_angle_other_deg1.3261.58517572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765948
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69922.541370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.215151456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0831542
X-RAY DIFFRACTIONr_chiral_restr0.1440.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021572
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A71310.12
12B71310.12
21A78630.08
22C78630.08
31A73430.12
32D73430.12
41B71510.12
42C71510.12
51B74680.07
52D74680.07
61C73550.12
62D73550.12
LS refinement shellResolution: 1.582→1.623 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 35 -
Rwork0.297 522 -
all-557 -
obs--5.6 %

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