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- PDB-2qr9: Crystal Structure of the Estrogen Receptor Alpha Ligand Binding D... -

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Basic information

Entry
Database: PDB / ID: 2qr9
TitleCrystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with an Oxabicyclic Derivative Compound
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Protein-Ligand Complex / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Phosphorylation / Receptor / Steroid-binding / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression ...Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / HATs acetylate histones / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / Estrogen-dependent gene expression / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / mammary gland branching involved in pregnancy / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / androgen metabolic process / regulation of glucose metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / negative regulation of canonical NF-kappaB signal transduction / estrogen receptor signaling pathway / positive regulation of adipose tissue development / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / ESR-mediated signaling / : / transcription coregulator binding / response to progesterone / nuclear receptor binding / transcription corepressor binding / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / circadian regulation of gene expression / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / mRNA transcription by RNA polymerase II / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / circadian rhythm / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of fibroblast proliferation / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cytosolic calcium ion concentration / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 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 / 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-HZ3 / Estrogen receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsNettles, K.W. / Bruning, J.B.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: NFkappaB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses
Authors: Nettles, K.W. / Bruning, J.B. / Gil, G. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. / Katzenellenbogen, B.S. / Kim, Y. / Joachmiak, A. / Greene, G.L.
History
DepositionJul 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7226
Polymers61,9334
Non-polymers7892
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-26.6 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.987, 84.002, 58.724
Angle α, β, γ (deg.)90.000, 108.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29386.609 Da / Num. of mol.: 2 / Fragment: Steroid-binding region, residues 298-554 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q8BN74, UniProt: Q61026*PLUS
#3: Chemical ChemComp-HZ3 / dimethyl (1R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate


Mass: 394.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H18O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris 8.5, 0.2M Magnesium Hexahydrate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 3, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 31055 / Num. obs: 31055 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 28.72 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 18.65
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 10.65 / Num. unique all: 3192 / Rsym value: 0.156 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ERD

3erd


Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 12.586 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.263 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1552 5 %RANDOM
Rwork0.214 ---
obs0.216 30981 89.07 %-
all-29429 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.465 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å2-0.35 Å2
2--2.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 58 159 4195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214167
X-RAY DIFFRACTIONr_bond_other_d0.0010.022762
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9995651
X-RAY DIFFRACTIONr_angle_other_deg0.9923.0016761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14923.929168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05315772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5411522
X-RAY DIFFRACTIONr_chiral_restr0.0830.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
X-RAY DIFFRACTIONr_nbd_refined0.2290.2994
X-RAY DIFFRACTIONr_nbd_other0.1870.22714
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21958
X-RAY DIFFRACTIONr_nbtor_other0.0910.22064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.210
X-RAY DIFFRACTIONr_mcbond_it0.8381.52632
X-RAY DIFFRACTIONr_mcbond_other0.1711.51020
X-RAY DIFFRACTIONr_mcangle_it1.31524083
X-RAY DIFFRACTIONr_scbond_it1.93331733
X-RAY DIFFRACTIONr_scangle_it2.9944.51559
LS refinement shellResolution: 2→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 123 -
Rwork0.263 2211 -
all-2334 -
obs-2211 94.15 %
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)
16.5861-0.35843.86352.8448-0.50234.9673-0.44720.5275-0.3003-0.45290.25430.0393-0.2927-0.05220.19290.2235-0.07140.11380.1525-0.02040.032416.6289-0.4695-9.566
21.4203-0.12411.20143.18080.49253.1186-0.06680.1542-0.1257-0.339-0.019-0.00750.00610.0090.08580.2634-0.0320.10450.0997-0.00180.080611.6336-2.6855-6.6746
33.9888-0.80311.01315.4254-0.91771.6633-0.23990.18870.235-0.06130.13110.2237-0.3157-0.10790.10880.29370.00650.06420.11490.02680.055111.61916.57310.444
458.1212-105.48269.0262211.50564.377122.87480.90150.16191.55760.9223-0.0776-3.84681.2461.7081-0.8240.76770.04270.21320.84630.16950.736110.1628-21.00189.3732
53.08660.29851.10441.09290.18921.7855-0.00110.13530.0047-0.1261-0.0050.02930.0538-0.07150.00610.1955-0.00020.09040.11880.02040.12212.1427-3.27123.8661
65.44912.43260.41422.68490.1740.7566-0.0133-0.28910.17220.266-0.02510.26520.04810.10070.03840.21790.02160.08640.1107-0.01520.09160.0853-3.150630.1077
71.86740.3095-0.63872.4331-0.09531.0706-0.0431-0.0863-0.1142-0.01370.04120.02570.02560.00650.00190.19610.01280.07710.11150.010.1242.6568-3.101223.1008
812.97080.0960.69884.5594-6.31938.81180.34270.76960.8672-0.1848-0.68061.1564-1.1728-0.30460.33790.78110.18780.20250.5585-0.01570.54099.917117.96612.6731
93.66960.1729-0.37160.8045-0.20820.1677-0.0149-0.09060.0830.010.00120.01960.0308-0.00080.01370.19240.01350.06710.1433-0.00190.13398.0942-0.040117.8236
1085.479218.481826.974326.426514.913469.9859-0.17654.0621-1.8304-2.56011.11580.0618-0.378-3.0537-0.93940.29370.0012-0.05830.5033-0.0410.2444-7.32446.31559.9402
1167.7077-27.71032.417332.53418.452220.85330.8660.9353-3.4541-1.8904-0.64762.02230.614-0.5861-0.21840.4133-0.0209-0.0561-0.035-0.08780.15927.4111-18.3132-10.9896
1218.38187.9205-12.981725.6236-4.36618.12150.51310.03821.680.22630.09961.6577-0.9903-0.9434-0.61270.15750.06650.13420.0496-0.04850.3197-6.717415.813425.9157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA305 - 3439 - 47
2X-RAY DIFFRACTION2AA344 - 41048 - 114
3X-RAY DIFFRACTION3AA411 - 458115 - 162
4X-RAY DIFFRACTION4AA459 - 468163 - 172
5X-RAY DIFFRACTION5AA469 - 549173 - 253
6X-RAY DIFFRACTION6BB306 - 34610 - 50
7X-RAY DIFFRACTION7BB347 - 45851 - 162
8X-RAY DIFFRACTION8BB459 - 472163 - 176
9X-RAY DIFFRACTION9BB473 - 544177 - 248
10X-RAY DIFFRACTION10BB545 - 550249 - 254
11X-RAY DIFFRACTION11CC687 - 6962 - 11
12X-RAY DIFFRACTION12DD686 - 6961 - 11

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