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- PDB-1zaf: Crystal structure of estrogen receptor beta complexed with 3-Brom... -

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Basic information

Entry
Database: PDB / ID: 1zaf
TitleCrystal structure of estrogen receptor beta complexed with 3-Bromo-6-hydroxy-2-(4-hydroxy-phenyl)-inden-1-one
Components
  • Estrogen receptor beta
  • Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION/TRANSFERASE / estrogen receptor / estrogen receptor beta / er-beta / er / estrogen / nuclear receptor / transcription factor / agonist / TRANSCRIPTION-TRANSFERASE COMPLEX
Function / homology
Function and homology information


receptor antagonist activity / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity / hypothalamus development / male mating behavior / nuclear steroid receptor activity / progesterone receptor signaling pathway / response to progesterone ...receptor antagonist activity / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity / hypothalamus development / male mating behavior / nuclear steroid receptor activity / progesterone receptor signaling pathway / response to progesterone / Synthesis of bile acids and bile salts / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cerebellum development / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / protein-lysine-acetyltransferase activity / nuclear retinoid X receptor binding / lactation / positive regulation of neuron differentiation / estrous cycle / estrogen receptor signaling pathway / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / cellular response to hormone stimulus / steroid binding / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / positive regulation of adipose tissue development / bile acid and bile salt transport / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / male gonad development / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / ESR-mediated signaling / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / cellular response to estradiol stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / cerebral cortex development / negative regulation of cell growth / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coregulator activity / Constitutive Signaling by Aberrant PI3K in Cancer / response to estradiol / PIP3 activates AKT signaling / cell-cell signaling / transcription regulator complex / HATs acetylate histones / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / Extra-nuclear estrogen signaling / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 1 / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 1 / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / : / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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-789 / Nuclear receptor coactivator 1 / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMcDevitt, R.E. / Malamas, M.S. / Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Miller, C.P. / Harris, H.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Estrogen receptor ligands: design and synthesis of new 2-arylindene-1-ones
Authors: McDevitt, R.E. / Malamas, M.S. / Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Miller, C.P. / Harris, H.A.
History
DepositionApr 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 beta
B: Estrogen receptor beta
C: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2216
Polymers56,5874
Non-polymers6342
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-42 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.281, 89.213, 99.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Estrogen receptor beta / ER-beta


Mass: 26906.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q92731
#2: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Steroid receptor coactivator-1 / SRC-1 / RIP160 / Hin-2 protein


Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence was derived from steroid receptor coactivator-1.
References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-789 / 3-BROMO-6-HYDROXY-2-(4-HYDROXYPHENYL)-1H-INDEN-1-ONE


Mass: 317.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H9BrO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 15% PEG3350, 0.2M Mg Acetate, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.2 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 26, 1999 / Details: monochromator
RadiationMonochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 24154 / Num. obs: 23329 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 15.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.08 / Num. unique all: 1151 / Rsym value: 0.348 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→14.91 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2465802.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: OTHER REFINEMENT REMARKS: NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1136 4.9 %RANDOM
Rwork0.226 ---
all0.229 24154 --
obs0.226 23329 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9415 Å2 / ksol: 0.364206 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--7.38 Å20 Å2
3----7.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 38 167 4001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_mcbond_it0.821.5
X-RAY DIFFRACTIONc_mcangle_it1.42
X-RAY DIFFRACTIONc_scbond_it1.142
X-RAY DIFFRACTIONc_scangle_it1.712.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.340.3161714.70.24934623462
2.34-2.520.3081770.2473629
2.52-2.770.3082010.2473658
2.77-3.170.2931820.2453710
3.17-3.980.2861880.2143802
3.98-150.2562170.2063932
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4789.par789.top

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