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- PDB-1err: HUMAN ESTROGEN RECEPTOR LIGAND-BINDING DOMAIN IN COMPLEX WITH RAL... -

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Basic information

Entry
Database: PDB / ID: 1err
TitleHUMAN ESTROGEN RECEPTOR LIGAND-BINDING DOMAIN IN COMPLEX WITH RALOXIFENE
ComponentsESTROGEN RECEPTOR
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / STEROID / ANTAGONIST
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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / 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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / 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 / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / 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 / Extra-nuclear estrogen signaling / calmodulin binding / 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 / 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 / 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 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RALOXIFENE / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsBrzozowski, A.M. / Pike, A.C.W.
CitationJournal: Nature / Year: 1997
Title: Molecular basis of agonism and antagonism in the oestrogen receptor.
Authors: Brzozowski, A.M. / Pike, A.C. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustafsson, J.A. / Carlquist, M.
History
DepositionSep 8, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2013Group: Atomic model
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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
B: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8414
Polymers57,8942
Non-polymers9472
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-13 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.530, 53.680, 102.710
Angle α, β, γ (deg.)90.00, 116.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-373-

HIS

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.740953, -0.502251, 0.445794), (-0.502316, -0.026089, -0.86429), (0.445721, -0.864328, -0.232958)
Vector: 74.861, 122.904, 94.95)

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Components

#1: Protein ESTROGEN RECEPTOR / ESTROGEN RECEPTOR / ER-LBD / ER-ALPHA


Mass: 28947.057 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: LIGAND-BINDING DOMAIN (DOMAIN E - RESIDUES 301-553) IN COMPLEX WITH THE SELECTIVE ANTAGONIST RALOXIFENE
Source: (gene. exp.) Homo sapiens (human) / Strain: JM109 / Gene: ER ALPHA / Variant: C1857 / Plasmid: PEALPHA 35 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / Variant (production host): C1857 / References: UniProt: P03372
#2: Chemical ChemComp-RAL / RALOXIFENE


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


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5
Details: 12% (W/V) PEG 4000, 0.2M MAGNESIUM CHLORIDE, 50MM L-LYSINE, 0.1M SUCROSE, 5% 1,4-DIOXANE, 0.1M TRIS-HCL, PH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %(w/v)PEG40001reservoir
20.2 M1reservoirMgCl2
350 mML-lysine1reservoir
40.1 Msucrose1reservoir
55 %1,4-dioxane1reservoir
60.1 MTris-HCl1reservoir
77.2 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9054
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 9, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9054 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 15433 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 52.5 Å2 / Rsym value: 0.08 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.446 / % possible all: 62.6
Reflection
*PLUS
Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.6→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1565 10 %RANDOM
Rwork0.219 ---
obs-15433 95.7 %-
Displacement parametersBiso mean: 53.8 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 68 100 3670
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0520.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.7392
X-RAY DIFFRACTIONp_mcangle_it4.6393
X-RAY DIFFRACTIONp_scbond_it3.1062
X-RAY DIFFRACTIONp_scangle_it4.8283
X-RAY DIFFRACTIONp_plane_restr0.030.04
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.2050.3
X-RAY DIFFRACTIONp_multtor_nbd0.3130.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor3.17
X-RAY DIFFRACTIONp_staggered_tor22.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor39.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS

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