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

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Basic information

Entry
Database: PDB / ID: 5dxk
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-[(9s)-bicyclo[3.3.1]non-9-ylmethanediyl]diphenol
Components
  • Estrogen receptor
  • Nuclear 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / 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 / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid 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 / 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 / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / 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 / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator 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 / 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-5J1 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.226 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
DepositionSep 23, 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: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5786
Polymers61,9334
Non-polymers6452
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-27 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.637, 82.538, 58.636
Angle α, β, γ (deg.)90.000, 111.050, 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 / Fragment: ligand-binding domain / 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 Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1666.943 Da / Num. of mol.: 2 / Fragment: Nuclear receptor-interacting peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-5J1 / 4,4'-[(9s)-bicyclo[3.3.1]non-9-ylmethanediyl]diphenol


Mass: 322.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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 Å3/Da / Density % sol: 38.44 %
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: Nov 22, 2013
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: 2.22→50 Å / Num. obs: 23460 / % possible obs: 98.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Χ2: 0.775 / Net I/av σ(I): 21.625 / Net I/σ(I): 4.9 / Num. measured all: 161268
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.22-2.266.70.5511650.9050.2220.5940.47998.5
2.26-2.36.90.47311550.930.190.510.49897.4
2.3-2.346.90.43611810.9420.1750.470.45498.2
2.34-2.396.90.41211580.9380.1660.4450.4798.8
2.39-2.446.90.33411710.9640.1340.3610.49499.1
2.44-2.56.90.30511780.9610.1230.3290.5299.3
2.5-2.566.90.28111620.9660.1140.3040.53799
2.56-2.636.80.23911840.9760.0980.2590.5599.3
2.63-2.716.70.20611660.980.0850.2240.57498.6
2.71-2.86.20.18211350.9760.0790.1990.58693.7
2.8-2.96.90.1611740.9880.0650.1730.63797.8
2.9-3.017.20.12711520.9920.050.1370.7199.5
3.01-3.157.20.11712080.9930.0470.1260.75499.6
3.15-3.3270.10811710.9920.0440.1170.83599.2
3.32-3.526.90.09111900.9930.0370.0980.95399.6
3.52-3.86.80.08211950.9940.0340.0891.09299.3
3.8-4.186.30.07811430.9940.0330.0851.30394.5
4.18-4.787.20.07711750.9940.0310.0831.36999.5
4.78-6.0270.07612010.9950.0310.0821.22599.2
6.02-506.80.05911960.9970.0240.0641.41496.3

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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: 2.226→46.57 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1935 8.56 %
Rwork0.1822 20658 -
obs0.186 22593 94.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.53 Å2 / Biso mean: 53.3189 Å2 / Biso min: 19.97 Å2
Refinement stepCycle: final / Resolution: 2.226→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3851 0 48 129 4028
Biso mean--38.99 47.14 -
Num. residues----492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033996
X-RAY DIFFRACTIONf_angle_d0.755414
X-RAY DIFFRACTIONf_chiral_restr0.026640
X-RAY DIFFRACTIONf_plane_restr0.004671
X-RAY DIFFRACTIONf_dihedral_angle_d12.8421463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2259-2.28150.30031210.22321310143183
2.2815-2.34320.30091370.21951372150990
2.3432-2.41220.26261240.22191439156392
2.4122-2.490.25121390.20261457159694
2.49-2.5790.27541260.21071466159293
2.579-2.68230.24571450.21231463160894
2.6823-2.80430.30341290.23021434156392
2.8043-2.95210.26611460.21831482162896
2.9521-3.13710.21661400.20741526166698
3.1371-3.37920.25421410.20451558169999
3.3792-3.71920.22641470.1811546169399
3.7192-4.2570.17651450.14971493163896
4.257-5.36210.19161500.146315631713100
5.3621-46.58010.21821450.16491549169496
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)
12.5848-0.8413-1.01186.18751.21054.05890.01310.61760.9458-0.22540.14850.5609-1.1058-0.8579-0.20920.59210.3164-0.05410.73020.14430.56220.256517.8531-5.6081
28.4533-7.58171.78199.1955-0.82911.49420.2360.4351-0.3744-0.1769-0.3204-0.54040.37520.1844-0.07450.46820.10830.04590.45640.03560.542520.9959-6.3369-6.844
34.7039-1.3145-2.80155.43571.43684.63570.19390.1454-0.0589-0.30750.0004-0.1507-0.09330.2517-0.27340.2204-0.0392-0.05410.287-0.01430.25720.69242.8208-1.2784
44.07660.6327-0.95923.74571.2574.8383-0.03290.1436-0.1798-0.0262-0.0140.07790.1996-0.08220.05980.20650.0244-0.00610.27010.00880.246513.73920.66262.8638
53.4569-5.25893.10739.498-2.36688.6280.21810.4272-1.1372-0.3272-0.11270.51510.9929-0.40460.00070.3961-0.070.09240.31460.00220.37635.2292-7.74316.5348
64.5777-0.3973-1.93742.6316-0.51722.08350.2220.24490.2391-0.1874-0.19730.0829-0.6447-0.7719-0.01390.38370.136-0.00710.40080.07220.3217-0.080811.62374.017
76.7428-1.35050.13591.9503-0.13733.33370.32710.0775-0.43730.003-0.2170.10360.4551-0.0172-0.06830.3094-0.0135-0.02720.2781-0.00550.23836.02381.564211.188
87.30690.3771-1.39373.5561-0.74785.97550.0672-0.76710.1788-0.3042-0.0268-0.28430.48690.96660.03340.32590.006-0.07190.51170.04770.461727.68254.13078.6889
95.16691.18314.34854.2125-1.41319.03640.370.0339-1.0440.06250.30190.84340.2039-1.5196-0.69370.3882-0.16240.11880.8981-0.14530.7493-17.64391.790825.5947
102.8460.64043.34381.82781.34674.3777-0.29420.5544-0.25520.23410.4869-0.7213-0.45911.0683-0.02360.53090.0754-0.07290.665-0.10340.49688.921710.524443.9441
112.4425-0.5707-0.54454.20281.56526.1029-0.2193-0.1593-0.35780.3702-0.01960.34690.57710.04460.20540.33940.00250.07640.31570.00520.27232.08821.943832.1061
124.08110.3542-0.25263.0721.25125.9093-0.0410.00690.2625-0.06440.1968-0.3193-0.6860.3154-0.08310.3998-0.02620.05410.25-0.01890.29015.300812.931226.9997
135.64754.85835.07114.5264.47594.58470.9491-0.5906-0.07220.00420.1561-0.47330.1773-0.6434-0.48590.9163-0.01230.15310.4929-0.04470.6389-1.391-10.115.6031
144.4506-1.27370.43722.7984-0.76155.6413-0.10320.0473-0.0505-0.01840.01060.1045-0.1305-0.44730.04440.27260.01740.03190.2514-0.06410.2235-1.32546.214918.5985
156.04740.4244-1.90953.0865-1.11785.3046-0.5885-0.7108-0.67870.3840.1279-0.37891.10841.58120.15390.76420.29850.07070.75230.18040.612814.206-6.440432.9196
164.76630.67264.30990.63790.97054.19480.56530.4283-0.09970.2772-1.0597-0.1025-0.86961.90230.01580.5841-0.12320.23710.5470.07890.82325.50317.56921.0709
177.1862-1.53265.62076.2276-0.26434.5423-0.5693-1.3817-2.80750.26320.27860.41592.3812-0.52790.11731.06550.01590.2620.51370.13740.85510.5415-13.522235.4275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 321 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 363 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 421 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 438 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 439 through 496 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 530 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 531 through 548 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 305 through 321 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 322 through 339 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 340 through 407 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 408 through 455 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 456 through 471 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 472 through 531 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 532 through 549 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 687 through 696 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 688 through 696 )D0

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