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- PDB-2ouz: Crystal Structure of Estrogen Receptor alpha-lasofoxifene complex -

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Basic information

Entry
Database: PDB / ID: 2ouz
TitleCrystal Structure of Estrogen Receptor alpha-lasofoxifene complex
ComponentsEstrogen receptor
KeywordsHORMONE/GROWTH FACTOR / Nuclear receptor / SERM / estrogen / HORMONE-GROWTH FACTOR 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 / 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 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C3D / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVajdos, F.F. / Pandit, J.
CitationJournal: Protein Sci. / Year: 2007
Title: The 2.0 A crystal structure of the ER{alpha} ligand-binding domain complexed with lasofoxifene
Authors: Vajdos, F.F. / Hoth, L.R. / Geoghegan, K.F. / Simons, S.P. / LeMotte, P.K. / Danley, D.E. / Ammirati, M.J. / Pandit, J.
History
DepositionFeb 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jan 15, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3032
Polymers28,8891
Non-polymers4141
Water2,900161
1
A: Estrogen receptor
hetero molecules

A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6054
Polymers57,7782
Non-polymers8272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)58.306, 58.306, 275.033
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Estrogen receptor / ER / Estradiol receptor / ER-alpha


Mass: 28889.021 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain, residues 306-551
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-C3D / (5R,6S)-6-PHENYL-5-[4-(2-PYRROLIDIN-1-YLETHOXY)PHENYL]-5,6,7,8-TETRAHYDRONAPHTHALEN-2-OL / Lasofoxifene


Mass: 413.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H31NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1 M NaHEPES, 0.5 M NaCl, 6% ethylene glycol, 10-12%PEG 8000, 5mM DTT, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 3, 1999 / Details: osmic
RadiationMonochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50.64 Å / Num. all: 19969 / Num. obs: 18869 / % possible obs: 94.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.25 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 1.61 / % possible all: 87.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ERT

3ert


Resolution: 2→50.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.77 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 976 5.2 %RANDOM
Rwork0.199 ---
obs0.202 18800 94.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.12 Å2
Refine analyzeLuzzati coordinate error obs: 0.308 Å
Refinement stepCycle: LAST / Resolution: 2→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 31 161 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212013
X-RAY DIFFRACTIONr_bond_other_d0.0010.021898
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9972727
X-RAY DIFFRACTIONr_angle_other_deg0.96134396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.15424.14682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9215364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2481510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_nbd_refined0.2440.2534
X-RAY DIFFRACTIONr_nbd_other0.1850.21967
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2982
X-RAY DIFFRACTIONr_nbtor_other0.0910.21194
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2410.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5490.219
X-RAY DIFFRACTIONr_mcbond_it1.1281.51273
X-RAY DIFFRACTIONr_mcbond_other0.2741.5496
X-RAY DIFFRACTIONr_mcangle_it1.84121971
X-RAY DIFFRACTIONr_scbond_it2.5243847
X-RAY DIFFRACTIONr_scangle_it3.5284.5756
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 71 -
Rwork0.271 1138 -
obs-1209 85.93 %
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)
11.5117-0.4853-0.17633.1097-0.15482.8193-0.0066-0.0508-0.06550.0392-0.04520.06640.2063-0.11980.0518-0.185-0.09430.0077-0.2176-0.0131-0.198422.02066.479223.1147
220.87230.6013.595911.84584.3256.93620.1048-0.235-0.5558-0.6407-0.1708-0.45810.52490.46550.0660.12260.0161-0.0012-0.1033-0.0085-0.190828.9216-2.51148.881
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A306 - 5286 - 228
21B9991
32A536 - 544236 - 244

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