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- PDB-4pps: Crystal Structure of the Estrogen Receptor alpha Ligand-binding D... -

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Basic information

Entry
Database: PDB / ID: 4pps
TitleCrystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with an A-CD ring estrogen derivative
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsPROTEIN BINDING / nuclear hormone receptor / transcription factor / ligand-binding / nucleus
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
Chem-ESE / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. ...Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W.
CitationJournal: Elife / Year: 2014
Title: Resveratrol modulates the inflammatory response via an estrogen receptor-signal integration network.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: Estrogen receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0606
Polymers58,5674
Non-polymers4932
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-29 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.106, 84.191, 58.480
Angle α, β, γ (deg.)90.00, 108.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Estrogen receptor / Estrogen receptor alpha / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 27832.783 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (UNP residues 305-548) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1450.686 Da / Num. of mol.: 2
Fragment: receptor-interacting peptide (UNP residues 687-698)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-ESE / (1S,3aR,5R,7aS)-5-(4-hydroxyphenyl)-7a-methyloctahydro-1H-inden-1-ol


Mass: 246.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H22O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 15% PEG3350, 0.05 M magnesium chloride, 0.067 M sodium chloride, 0.1 M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.929→33.541 Å / Num. all: 38369 / Num. obs: 38369 / % possible obs: 98.68 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.7
Reflection shellResolution: 1.929→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3443 / % possible all: 89.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QA8

2qa8


Resolution: 1.929→33.541 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 1883 5.2 %RANDOM
Rwork0.1766 ---
all0.1779 38369 --
obs0.1779 36236 93.22 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.511 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1438 Å20 Å26.6831 Å2
2--2.76 Å2-0 Å2
3----3.9038 Å2
Refinement stepCycle: LAST / Resolution: 1.929→33.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 36 323 4296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024140
X-RAY DIFFRACTIONf_angle_d0.6145614
X-RAY DIFFRACTIONf_dihedral_angle_d12.9081555
X-RAY DIFFRACTIONf_chiral_restr0.044659
X-RAY DIFFRACTIONf_plane_restr0.002699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.929-1.98160.27951060.24192060X-RAY DIFFRACTION73
1.9816-2.03990.23591170.21182350X-RAY DIFFRACTION84
2.0399-2.10570.23911450.19052517X-RAY DIFFRACTION89
2.1057-2.1810.21311490.18842628X-RAY DIFFRACTION93
2.181-2.26830.26091360.20952436X-RAY DIFFRACTION87
2.2683-2.37150.20811340.18092676X-RAY DIFFRACTION95
2.3715-2.49650.24151610.17862735X-RAY DIFFRACTION97
2.4965-2.65280.22941530.18012793X-RAY DIFFRACTION98
2.6528-2.85750.23421570.18882763X-RAY DIFFRACTION99
2.8575-3.14490.20471530.17892836X-RAY DIFFRACTION100
3.1449-3.59950.2061520.17282837X-RAY DIFFRACTION100
3.5995-4.53330.15151610.14842851X-RAY DIFFRACTION100
4.5333-33.54590.1791590.17452871X-RAY DIFFRACTION99
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)
10.0119-0.01330.02120.0492-0.02720.01810.2951-0.4633-0.39060.1064-0.0620.33850.4493-0.5278-0.00010.3221-0.0540.00690.4540.05120.4316-11.0929-7.109929.4648
20.5111-0.4234-0.12850.36180.07740.02820.2522-0.28980.23280.4467-0.0662-0.2833-0.70050.44020.2710.6632-0.19580.00470.4623-0.08680.271111.5299.548245.76
30.81430.13160.73560.8891-0.67571.21210.0143-0.0846-0.20750.125-0.01590.00260.1584-0.0038-0.01160.2587-0.0099-0.00190.1849-0.00720.21218.1519-4.058433.996
41.1138-0.21690.21280.8677-0.41170.9904-0.2368-0.25020.19250.5013-0.0564-0.3417-0.68370.31-0.17210.4475-0.0744-0.0650.1934-0.03780.247412.664614.755135.5612
50.12890.16890.01470.1922-0.02670.0576-0.0930.15820.533-0.2787-0.0399-0.0856-0.55520.1185-0.00020.3266-0.04410.00310.2427-0.03210.24149.462313.237725.7553
60.27630.14220.34050.14220.08540.3743-0.09460.0752-0.1030.0465-0.01920.30970.0094-0.28830.00010.21470.03230.00470.2322-0.0210.2182-1.84331.743725.5906
71.9478-1.2112.01610.8411-1.23212.46280.2020.0435-0.5463-0.48550.29330.04340.95180.51730.32720.3981-0.0720.04310.6818-0.16160.41848.3568-14.565818.9675
81.00880.3114-0.20950.47960.05241.0696-0.12030.0143-0.4498-0.0334-0.09680.33280.5669-0.3942-0.07560.225-0.02860.00410.2813-0.01680.2718-6.8661-6.324219.2448
90.46070.4172-0.47151.15510.21640.78840.1391-0.03370.30970.0259-0.1529-0.0843-0.0410.14260.00150.1905-0.0318-0.00220.2073-0.02710.18798.94243.743321.3733
100.277-0.42990.14270.8875-0.53051.20170.18290.1897-0.1689-0.0233-0.4456-1.01620.11531.1987-0.05110.4352-0.0342-0.08620.48490.02430.422221.9483-5.237636.0876
110.3846-0.0996-0.41480.955-0.37670.40720.07320.380.2926-0.1801-0.0567-0.319-0.01180.01320.0370.30570.0138-0.0070.22640.00870.204215.62890.1509-4.2167
121.2264-0.045-0.54871.70090.26251.15290.02250.05420.0009-0.1024-0.0217-0.01510.00160.0182-0.00010.1602-0.0086-0.00290.157-0.00870.156118.9483-2.69154.7412
131.6497-0.4607-0.8790.79710.17270.73540.06480.01950.3023-0.0289-0.0111-0.0501-0.0853-0.06390.00270.135-0.0108-0.00640.15770.00490.170410.15382.8879.5667
143.13782.19792.7834.24052.89462.80430.4705-0.7641-0.320.5298-0.20770.81070.7346-0.9701-0.07040.56720.0593-0.02090.32450.08580.24459.6719-16.220239.2206
150.12-0.023-0.06970.01510.03230.1243-0.00890.19530.4527-0.41410.033-0.7075-0.58550.61940.00710.34350.02910.10350.29310.08310.430324.600217.11271.0381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 305:322 )
2X-RAY DIFFRACTION2chain 'A' and (resid 323:338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339:395 )
4X-RAY DIFFRACTION4chain 'A' and (resid 396:421 )
5X-RAY DIFFRACTION5chain 'A' and (resid 422:437 )
6X-RAY DIFFRACTION6chain 'A' and (resid 438:455 )
7X-RAY DIFFRACTION7chain 'A' and (resid 456:468 )
8X-RAY DIFFRACTION8chain 'A' and (resid 469:496 )
9X-RAY DIFFRACTION9chain 'A' and (resid 497:530 )
10X-RAY DIFFRACTION10chain 'A' and (resid 531:548 )
11X-RAY DIFFRACTION11chain 'B' and (resid 305:338 )
12X-RAY DIFFRACTION12chain 'B' and (resid 339:438 )
13X-RAY DIFFRACTION13chain 'B' and (resid 439:548 )
14X-RAY DIFFRACTION14chain 'C' and (resid 687:698 )
15X-RAY DIFFRACTION15chain 'D' and (resid 688:696 )

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