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- PDB-2j7x: STRUCTURE OF ESTRADIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 2j7x
TitleSTRUCTURE OF ESTRADIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN COMPLEX WITH LXXLL MOTIF FROM NCOA5
Components
  • ESTROGEN RECEPTOR BETA
  • NUCLEAR RECEPTOR COACTIVATOR 5NCOA5
KeywordsTRANSCRIPTION / ZINC-FINGER / NUCLEAR RECEPTOR / PHOSPHORYLATION / STEROID-BINDING / GLYCOPROTEIN / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


negative regulation of behavior / cellular response to magnetism / response to bisphenol A / PIP3 activates AKT signaling / estrogen binding / estradiol binding / response to insecticide / response to human chorionic gonadotropin / epithelial cell maturation involved in prostate gland development / hormone-mediated apoptotic signaling pathway ...negative regulation of behavior / cellular response to magnetism / response to bisphenol A / PIP3 activates AKT signaling / estrogen binding / estradiol binding / response to insecticide / response to human chorionic gonadotropin / epithelial cell maturation involved in prostate gland development / hormone-mediated apoptotic signaling pathway / amygdala development / Extra-nuclear estrogen signaling / Sertoli cell proliferation / ESR-mediated signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Sertoli cell development / prostate gland development / organic cyclic compound binding / response to genistein / hormone binding / Nuclear Receptor transcription pathway / response to salt / negative regulation of androgen receptor signaling pathway / steroid hormone binding / prostate gland epithelium morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / hypothalamus development / nuclear steroid receptor activity / female gonad development / heterocyclic compound binding / response to testosterone / response to dexamethasone / nuclear estrogen receptor activity / negative regulation of feeding behavior / androgen receptor signaling pathway / uterus development / vagina development / estrous cycle / cellular response to organic cyclic compound / negative regulation of reactive oxygen species metabolic process / behavioral fear response / regulation of signal transduction / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / ovarian follicle development / negative regulation of insulin receptor signaling pathway / steroid binding / cerebellum development / response to hormone / response to nutrient levels / response to activity / epithelial cell proliferation / cellular response to estradiol stimulus / negative regulation of smooth muscle cell proliferation / promoter-specific chromatin binding / protein-DNA complex / brain development / neuron migration / response to organic cyclic compound / vasodilation / response to estrogen / transcription corepressor activity / male gonad development / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / negative regulation of epithelial cell proliferation / cellular response to xenobiotic stimulus / actin cytoskeleton / glucose homeostasis / response to estradiol / insulin receptor signaling pathway / regulation of cell population proliferation / perikaryon / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / cellular response to lipopolysaccharide / cell population proliferation / negative regulation of neuron apoptotic process / sequence-specific DNA binding / positive regulation of ERK1 and ERK2 cascade / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / neuronal cell body / chromatin binding / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / extracellular space / RNA 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 / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...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 / Zinc finger, C4 type (two domains) / 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 / ESTRADIOL / 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: 2.1 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: Refinement description / 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)31,3019
Polymers30,6232
Non-polymers6787
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint5.8 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.550, 62.550, 171.700
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-2081-

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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GI724 / References: UniProt: Q62986
#2: Protein/peptide NUCLEAR RECEPTOR COACTIVATOR 5 / NCOA5 / 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, 105 molecules

#3: Chemical ChemComp-EST / ESTRADIOL / Estradiol


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.74 Å3/Da / Density % sol: 55 %
Crystal growpH: 8
Details: 5-7% PEG 8K, 5-7% PEG 1K, 0.13M LITHIUM SULPHATE, 0.1M TRIS PH 8.0 .

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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: 2.1→40 Å / Num. obs: 20776 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 15 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5 / % 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: 2.1→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.751 / SU ML: 0.096 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1056 5.1 %RANDOM
Rwork0.19 ---
obs0.192 19670 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 45 98 1994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221942
X-RAY DIFFRACTIONr_bond_other_d0.0010.021300
X-RAY DIFFRACTIONr_angle_refined_deg1.3912.0152619
X-RAY DIFFRACTIONr_angle_other_deg1.69233221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8195235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80524.78369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15415371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.368158
X-RAY DIFFRACTIONr_chiral_restr0.0830.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined0.2220.2424
X-RAY DIFFRACTIONr_nbd_other0.1770.21255
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2954
X-RAY DIFFRACTIONr_nbtor_other0.0880.2903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8941.51260
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33221927
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0913806
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0184.5692
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 70
Rwork0.17 1423
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.18710.08110.1331.4656-0.4212.5218-0.0089-0.0485-0.3011-0.02050.05210.11270.2814-0.2167-0.0432-0.1965-0.0429-0.0071-0.11920.0001-0.188951.392641.1176.5602
229.2416.17771.939250.137311.054213.83310.3471-2.9677-0.94432.6511-0.50810.3921.1126-0.33430.161-0.0948-0.0210.05070.43160.2015-0.030237.63542.3891.6876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A217 - 453
2X-RAY DIFFRACTION2B5 - 15

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