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- PDB-2qe4: Estrogen receptor alpha ligand-binding domain in complex with a b... -

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Basic information

Entry
Database: PDB / ID: 2qe4
TitleEstrogen receptor alpha ligand-binding domain in complex with a benzopyran agonist
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / nuclear receptor / ligand-binding domain / Alternative splicing / DNA-binding / Lipid-binding / Metal-binding / Nuclear protein / Phosphorylation / Polymorphism / Steroid-binding / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / Developmental Lineage of Mammary Gland Alveolar Cells / TFIIB-class transcription factor binding / negative regulation of smooth muscle cell apoptotic process / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells ...steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / Developmental Lineage of Mammary Gland Alveolar Cells / TFIIB-class transcription factor binding / negative regulation of smooth muscle cell apoptotic process / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / Nuclear signaling by ERBB4 / estrogen receptor signaling pathway / RNA polymerase II preinitiation complex assembly / steroid binding / positive regulation of nitric-oxide synthase activity / stem cell differentiation / protein localization to chromatin / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 14-3-3 protein binding / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nuclear estrogen receptor binding / nitric-oxide synthase regulator activity / transcription corepressor binding / transcription coregulator binding / negative regulation of canonical NF-kappaB signal transduction / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / euchromatin / Nuclear Receptor transcription pathway / response to estrogen / beta-catenin binding / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / sequence-specific double-stranded DNA binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / Golgi apparatus / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / zinc ion binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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
Chem-JJ3 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNorman, B.H. / Richardson, T.I. / Dodge, J.A. / Pfeifer, L.A. / Durst, G.L. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dinn, S.R. / Liu, S.Q. ...Norman, B.H. / Richardson, T.I. / Dodge, J.A. / Pfeifer, L.A. / Durst, G.L. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dinn, S.R. / Liu, S.Q. / Reilly, J.E. / Ryter, K.T.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 4: Functionalization of the benzopyran A-ring.
Authors: Norman, B.H. / Richardson, T.I. / Dodge, J.A. / Pfeifer, L.A. / Durst, G.L. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dinn, S.R. / Liu, S. / Reilly, J.E. / Ryter, K.T.
History
DepositionJun 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2474
Polymers56,5942
Non-polymers6532
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.915, 54.091, 84.169
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe ASU forms a biological assembly (dimer).

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Components

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


Mass: 28297.172 Da / Num. of mol.: 2 / Fragment: Ligand binding domain / Mutation: C381S, C417S, C530S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Chemical ChemComp-JJ3 / (3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-6-(METHOXYMETHYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL


Mass: 326.386 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM MES pH 6.8, 0.5 M MgCl2, 15% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→47.98 Å / Num. all: 18414 / Num. obs: 17217 / % possible obs: 93.5 % / Observed criterion σ(I): 2.54 / Redundancy: 2.7 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.55 / Num. unique all: 1813 / % possible all: 80.8

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Processing

Software
NameVersionClassification
CNX2005refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1689182.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1020 5.9 %RANDOM
Rwork0.241 ---
obs0.241 17216 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7202 Å2 / ksol: 0.38013 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--12.29 Å20 Å2-1.84 Å2
2--9.26 Å20 Å2
3---3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3274 0 48 31 3353
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 155 6.1 %
Rwork0.261 2382 -
obs--82.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2protein.top
X-RAY DIFFRACTION3water_rep.par
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5lig.par

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