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- PDB-2j7y: STRUCTURE OF 17-EPIESTRIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN CO... -

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Basic information

Entry
Database: PDB / ID: 2j7y
TitleSTRUCTURE OF 17-EPIESTRIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN COMPLEX WITH LXXLL MOTIF FROM NCOA5
Components
  • ESTROGEN RECEPTOR BETA
  • NUCLEAR RECEPTOR COACTIVATOR 5
KeywordsTRANSCRIPTION / RECEPTOR / ACTIVATOR / REPRESSOR / ZINC-FINGER / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / NUCLEAR PROTEIN / PHOSPHORYLATION / STEROID-BINDING / COACTIVATOR / COREPRESSOR / DNA-BINDING / GLYCOPROTEIN / TRANSCRIPTION REGULATION / METAL-BINDING / LIPID-BINDING
Function / homology
Function and homology information


negative regulation of behavior / cellular response to magnetism / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / response to bisphenol A / response to insecticide / estradiol binding / amygdala development / response to human chorionic gonadotropin ...negative regulation of behavior / cellular response to magnetism / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / response to bisphenol A / response to insecticide / estradiol binding / amygdala development / response to human chorionic gonadotropin / Extra-nuclear estrogen signaling / hormone-mediated apoptotic signaling pathway / epithelial cell maturation involved in prostate gland development / Sertoli cell proliferation / : / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Sertoli cell development / Nuclear Receptor transcription pathway / prostate gland development / response to genistein / steroid hormone binding / negative regulation of androgen receptor signaling pathway / hormone binding / response to salt / prostate gland epithelium morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / nuclear steroid receptor activity / hypothalamus development / nuclear estrogen receptor activity / heterocyclic compound binding / negative regulation of feeding behavior / female gonad development / uterus development / response to dexamethasone / vagina development / response to testosterone / androgen receptor signaling pathway / : / negative regulation of reactive oxygen species metabolic process / cellular response to estrogen stimulus / estrogen response element binding / behavioral fear response / regulation of signal transduction / nuclear receptor-mediated steroid hormone signaling pathway / estrous cycle / ovarian follicle development / negative regulation of insulin receptor signaling pathway / estrogen receptor signaling pathway / response to hormone / steroid binding / cerebellum development / epithelial cell proliferation / response to activity / positive regulation of DNA-binding transcription factor activity / promoter-specific chromatin binding / response to nicotine / cellular response to estradiol stimulus / negative regulation of smooth muscle cell proliferation / neuron migration / protein-DNA complex / response to nutrient levels / brain development / : / response to estrogen / nuclear receptor activity / male gonad development / vasodilation / negative regulation of epithelial cell proliferation / transcription corepressor activity / actin cytoskeleton / cellular response to xenobiotic stimulus / insulin receptor signaling pathway / glucose homeostasis / response to estradiol / regulation of cell population proliferation / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / perikaryon / negative regulation of neuron apoptotic process / sequence-specific DNA binding / positive regulation of ERK1 and ERK2 cascade / learning or memory / cell population proliferation / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding
Similarity search - Function
: / Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Anticodon-binding domain superfamily / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...: / Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Anticodon-binding domain superfamily / 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
BICARBONATE ION / Chem-E3O / Estrogen receptor beta / Nuclear receptor coactivator 5
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPike, A.C.W. / Brzozowski, A.M. / Hubbard, R.E. / Walton, J. / Bonn, T. / Thorsell, A.-G. / Engstrom, O. / Ljunggren, J. / Gustaffson, J.-A. / Carlquist, M.
CitationJournal: To be Published
Title: Structure of Agonist-Bound Estrogen Receptor Beta Lbd in Complex with Lxxll Motif from Ncoa5
Authors: Pike, A.C.W. / Brzozowski, A.M. / Hubbard, R.E. / Walton, J. / Bonn, T. / Thorsell, A.-G. / Engstrom, O. / Ljunggren, J. / Gustaffson, J.-A. / Carlquist, M.
History
DepositionOct 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESTROGEN RECEPTOR BETA
B: NUCLEAR RECEPTOR COACTIVATOR 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,44111
Polymers30,6232
Non-polymers8189
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.640, 62.640, 171.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-1462-

SO4

21A-2112-

HOH

31A-2126-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein ESTROGEN RECEPTOR BETA / ER-BETA


Mass: 28686.002 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 255-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PLEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GI724 / References: UniProt: Q62986
#2: Protein/peptide NUCLEAR RECEPTOR COACTIVATOR 5 / NCOA-5 / COACTIVATOR INDEPENDENT OF AF-2 / CIA / NCOA5


Mass: 1937.204 Da / Num. of mol.: 1 / Fragment: LXXLL PEPTIDE, RESIDUES 338-354 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9HCD5

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Non-polymers , 5 types, 172 molecules

#3: Chemical ChemComp-E3O / (16ALPHA,17ALPHA)-ESTRA-1,3,5(10)-TRIENE-3,16,17-TRIOL


Mass: 288.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growpH: 8
Details: 5-7%PEG8K, 5-7% PEG1K, 0.13M LITHIUM SULPHATE, 0.1M TRIS PH8.0, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 32671 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKN

1qkn


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.653 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1615 5 %RANDOM
Rwork0.184 ---
obs0.186 30570 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 54 163 2045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221935
X-RAY DIFFRACTIONr_bond_other_d0.0010.021306
X-RAY DIFFRACTIONr_angle_refined_deg1.3622.0192604
X-RAY DIFFRACTIONr_angle_other_deg1.95933237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2315231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65824.41268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.386159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.2240.2425
X-RAY DIFFRACTIONr_nbd_other0.1730.21304
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2955
X-RAY DIFFRACTIONr_nbtor_other0.0880.2898
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1760.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.18831243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.95551897
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0857817
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.44311707
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 116
Rwork0.218 2234
Refinement TLS params.Method: refined / Origin x: 50.9918 Å / Origin y: 41.446 Å / Origin z: 76.9937 Å
111213212223313233
T-0.1899 Å2-0.0327 Å20 Å2--0.128 Å20.0058 Å2---0.1458 Å2
L1.8644 °2-0.024 °20.1859 °2-1.2855 °2-0.3855 °2--2.1311 °2
S-0.005 Å °-0.0799 Å °-0.3013 Å °0.0205 Å °0.0609 Å °0.1323 Å °0.1947 Å °-0.1864 Å °-0.0559 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A217 - 453
2X-RAY DIFFRACTION1B343 - 351

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