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- PDB-1gwr: HUMAN OESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1gwr
TitleHUMAN OESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX WITH 17BETA-OESTRADIOL AND TIF2 NRBOX3 PEPTIDE
Components
  • OESTROGEN RECEPTOR
  • TRANSCRIPTION INTERMEDIARY FACTOR-2
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / TRANSACTIVATION / AGONIST / AF2 COACTIVATOR / RECEPTOR / ACTIVATOR / TRANSCRIPTI REGULATION / DNA-BINDING / NUCLEAR PROTEIN / ZINC FINGER / STER BINDING / PHOSPHORYLATION / POLYMORPHISM / ALTERNATIVE SPLICING
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Mitochondrial unfolded protein response (UPRmt) / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / 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 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / : / steroid binding / positive regulation of adipose tissue development / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to estrogen / RNA polymerase II transcription regulator complex / 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 / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 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
ESTRADIOL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPike, A.C.W. / Brzozowski, A.M.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Interaction of Transcriptional Intermediary Factor 2 Nuclear Receptor Box Peptides with the Coactivator Binding Site of Estrogen Receptor Alpha.
Authors: Warnmark, A. / Treuter, E. / Gustafsson, J.-A. / Hubbard, R.E. / Brzozowski, A.M. / Pike, A.C.W.
#1: Journal: 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
DepositionMar 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: OESTROGEN RECEPTOR
B: OESTROGEN RECEPTOR
C: TRANSCRIPTION INTERMEDIARY FACTOR-2
D: TRANSCRIPTION INTERMEDIARY FACTOR-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7716
Polymers58,2274
Non-polymers5452
Water81145
1
A: OESTROGEN RECEPTOR
C: TRANSCRIPTION INTERMEDIARY FACTOR-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3863
Polymers29,1132
Non-polymers2721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: OESTROGEN RECEPTOR
D: TRANSCRIPTION INTERMEDIARY FACTOR-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3863
Polymers29,1132
Non-polymers2721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.310, 90.540, 59.230
Angle α, β, γ (deg.)90.00, 109.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.7615, 0.07627, 0.64366), (0.0866, -0.99612, 0.01558), (0.64235, 0.04388, -0.76515)
Vector: 0.14209, -0.46075, -0.70198)

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Components

#1: Protein OESTROGEN RECEPTOR / ER / ESTRADIOL RECEPTOR / ER-ALPHA


Mass: 28022.037 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN RESIDUES 305-549
Source method: isolated from a genetically manipulated source
Details: LIGAND-BINDING DOMAIN (DOMAIN E - RESIDUES 260-500) IN COMPLEX WITH THE AGONIST 17BETA-OESTRADIOL
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEALPHA 35 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): C1857 / References: UniProt: P03372
#2: Protein/peptide TRANSCRIPTION INTERMEDIARY FACTOR-2 / TIF2


Mass: 1091.282 Da / Num. of mol.: 2 / Fragment: NUCLEAR RECEPTOR BOX III RESIDUES 742-750 / Source method: obtained synthetically
Details: TIF2 NR-BOX REGION 3 DERIVED PEPTIDE (RESIDUES 740-751)
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15596
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.41 Å3/Da / Density % sol: 48.5 %
Crystal growpH: 7.8 / Details: 2-2.5% (W/V) PEG 20000 0.1M HEPES PH7.8, pH 7.80
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 20680 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2 / % possible all: 82.9
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 134819
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 82.9 % / Num. unique obs: 915

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERE

1ere


Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.584 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: METHOD USED: BULK SOLVENT CONTRIBUTIONS CALCULATED BY XPLOR WERE INCORPORATE IN THE FORM OF PARTIAL STRUCTURE FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1052 5 %RANDOM
Rwork0.225 ---
obs-19611 95 %-
Displacement parametersBiso mean: 41.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 40 45 3973
LS refinement shellResolution: 2.4→2.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 123
Rwork0.28 -
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d0.038
LS refinement shell
*PLUS
Highest resolution: 2.404 Å / Lowest resolution: 2.518 Å / Num. reflection Rwork: 2289

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