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- PDB-5ehj: Crystal Structure of the ER-alpha Ligand-binding Domain in Comple... -

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Entry
Database: PDB / ID: 5ehj
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-[(4aR,8aR)-octahydronaphthalen-2(1H)-ylidenemethanediyl]diphenol
Components
  • Estrogen receptor
  • NCOA2Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
Function / homology
Function and homology information


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 / 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 / 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 / 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 / androgen metabolic process / TFIIB-class transcription factor binding / regulation of lipid metabolic process / steroid hormone mediated signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / intracellular steroid hormone receptor 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 / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / Regulation of lipid metabolism by PPARalpha / nitric-oxide synthase regulator activity / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / 14-3-3 protein binding / transcription corepressor binding / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / response to progesterone / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / positive regulation of nitric-oxide synthase activity / 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 / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / positive regulation of DNA-binding transcription factor activity / response to estrogen / RNA polymerase II transcription regulator complex / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / ATPase binding / positive regulation of cytosolic calcium ion concentration / 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 / 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. / Nuclear receptor coactivator, interlocking / 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-5K5 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. ...Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
CitationJournal: Mol.Syst.Biol. / Year: 2016
Title: Predictive features of ligand-specific signaling through the estrogen receptor.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: NCOA2
D: NCOA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6026
Polymers61,9334
Non-polymers6692
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-30 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.000, 81.990, 58.320
Angle α, β, γ (deg.)90.000, 110.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29299.535 Da / Num. of mol.: 2 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein/peptide NCOA2 / Nuclear receptor coactivator 2


Mass: 1666.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-5K5 / 4,4'-[(4aR,8aR)-octahydronaphthalen-2(1H)-ylidenemethanediyl]diphenol


Mass: 334.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.99 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2012
RadiationMonochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16733 / % possible obs: 98.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.78 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Χ2: 0.911 / Net I/av σ(I): 16.337 / Net I/σ(I): 4.9 / Num. measured all: 113908
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.5-2.546.98090.7440.4130.49398.7
2.54-2.596.98560.8250.3370.47499.10.830.897
2.59-2.646.88230.8940.2950.49598.30.720.779
2.64-2.696.78350.8850.2650.58198.60.6380.693
2.69-2.756.58450.9210.2180.52798.30.5180.563
2.75-2.825.87860.9280.2030.53394.50.4540.499
2.82-2.896.68230.9340.1720.56698.60.4120.448
2.89-2.967.28460.9670.1240.60499.40.310.334
2.96-3.057.18580.9770.1080.60699.80.2690.29
3.05-3.157.18190.9790.0950.69599.90.2380.257
3.15-3.267.18710.9830.0820.72599.70.2040.22
3.26-3.3978340.9890.0660.81199.60.1630.176
3.39-3.5578300.9840.0610.99398.90.1490.162
3.55-3.736.98450.990.0531.16198.30.1280.139
3.73-3.976.68270.9920.0461.299980.110.12
3.97-4.276.28150.9920.0431.35294.90.0990.108
4.27-4.77.28440.9920.0391.41499.40.0960.103
4.7-5.387.18500.9930.0381.47299.10.0940.101
5.38-6.786.88510.9910.0411.268990.0980.106
6.78-506.68660.9980.0282.10897.30.0670.073

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.459 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1532 10.05 %
Rwork0.2092 13716 -
obs0.2137 15248 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.25 Å2 / Biso mean: 41.6753 Å2 / Biso min: 2.35 Å2
Refinement stepCycle: final / Resolution: 2.5→46.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 50 108 3858
Biso mean--35.82 34.38 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023819
X-RAY DIFFRACTIONf_angle_d0.5395178
X-RAY DIFFRACTIONf_chiral_restr0.02625
X-RAY DIFFRACTIONf_plane_restr0.002639
X-RAY DIFFRACTIONf_dihedral_angle_d11.5461370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4936-2.5740.3275900.267285994962
2.574-2.6660.37251330.25671157129084
2.666-2.77280.26131240.25481176130084
2.7728-2.89890.28991410.25651189133086
2.8989-3.05170.2771500.24081296144694
3.0517-3.24290.30961480.24181326147495
3.2429-3.49320.27681470.22531288143595
3.4932-3.84460.25081490.19541324147395
3.8446-4.40060.2141500.1741325147595
4.4006-5.54280.22151520.17171391154399
5.5428-46.46720.20741480.19271385153397
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)
15.6702-3.7193-1.48098.19670.8592.65070.56710.8230.5852-0.9395-0.6296-0.5731-0.0351-0.2710.22270.24-0.0356-0.01950.35210.01590.1284-5.462120.1924-33.0609
23.6636-0.0298-0.6162.31961.13943.5938-0.14320.0882-0.18860.1271-0.1103-0.10110.36010.04360.21040.23580.00850.04370.18730.01270.1622-2.654915.9636-24.9404
34.7876-0.6672-0.50871.91970.58692.71380.02690.0270.0398-0.0542-0.0505-0.06750.1236-0.02110.06590.23150.02190.01120.17920.02280.1218-9.977121.8032-19.8549
46.0113-0.28122.73895.18071.8135.47870.0356-0.13130.4490.59330.90931.40920.0882-1.47820.03750.0953-0.1709-0.06450.61920.15730.4277-34.002315.7144-2.5772
54.3275-0.08790.75994.50111.14686.6163-0.1471-0.7437-0.25860.33180.1266-0.2740.19530.30220.07090.23950.08320.05480.24950.02460.2071-11.53919.149612.4783
63.0227-0.2476-0.46052.7182-0.18664.1463-0.0995-0.2941-0.3953-0.0742-0.1457-0.10850.23210.0390.17890.23350.01340.02140.20040.00410.1081-15.383516.97371.4401
76.0899-2.4216-5.14852.8699-0.49677.3919-0.1492-0.02770.35410.46571.2742-1.6726-1.9761.562-0.33750.2998-0.171-0.13620.7451-0.34480.4561-3.314530.35719.3579
82.99080.02060.95424.13750.91364.0454-0.05830.20310.1789-0.2107-0.0474-0.1409-0.6554-0.09780.0830.2209-0.00660.02950.27510.01110.1654-15.655326.907-2.9812
92.647-3.8441-1.43629.17161.47210.904-0.51390.3098-0.5557-1.4057-0.07281.14160.01620.61530.62481.2298-0.18050.0630.61-0.10210.4532-18.28863.2157-12.4554
104.2022-1.65570.24482.8201-0.42133.6029-0.1225-0.04710.1508-0.1016-0.0322-0.0257-0.1419-0.31340.14640.1781-0.00620.03960.2161-0.03160.1224-17.976421.8004-8.5507
116.50851.9375-1.54954.68320.01574.530.3544-0.56450.3634-0.4925-0.3821-1.86360.09340.9592-0.02960.55140.121-0.01310.40550.11190.7195-2.74228.62446.4207
128.9034-2.2991.96383.7881-1.48742.6014-0.1255-1.379-2.4454-0.2412-0.053-0.2431-0.011-0.48130.23130.5662-0.06740.04890.37170.19530.478-15.66121.00777.9462
134.7279-1.05421.54085.26832.77975.44841.0668-0.06870.7585-0.5722-0.1825-0.0737-0.91250.4254-0.3480.2728-0.07040.20550.37870.03760.52989.067932.5236-25.7319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 338 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 437 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 548 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 305 through 320 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 321 through 363 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 364 through 405 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 406 through 420 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 421 through 455 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 456 through 473 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 474 through 531 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 532 through 548 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 688 through 696 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 687 through 696 )D0

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