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- PDB-5e14: Crystal Structure of the ER-alpha Ligand-binding Domain in Comple... -

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Basic information

Entry
Database: PDB / ID: 5.0E+14
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-{[(3R)-3-phenylcyclohexylidene]methanediyl}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 / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / 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 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / 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 / 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 / beta-catenin binding / transcription coactivator 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-5KB / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / 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)62,6466
Polymers61,9334
Non-polymers7132
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-30 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.090, 81.849, 58.463
Angle α, β, γ (deg.)90.000, 110.980, 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-5KB / 4,4'-{[(3R)-3-phenylcyclohexylidene]methanediyl}diphenol


Mass: 356.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 38.28 %
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: Apr 3, 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: 23749 / % possible obs: 98.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.11 / Χ2: 1.604 / Net I/av σ(I): 25.125 / Net I/σ(I): 6.2 / Num. measured all: 155419
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.22-2.266.30.56311660.77699.7
2.26-2.36.50.63912240.6599.8
2.3-2.346.60.49311870.68699.7
2.34-2.396.70.47411880.69399.7
2.39-2.446.60.36911950.7899.7
2.44-2.56.60.35311890.86499.7
2.5-2.566.70.31211850.92199.2
2.56-2.636.70.27911821.01698.2
2.63-2.716.50.24211661.14497.7
2.71-2.860.21711611.29995.2
2.8-2.96.40.19911691.47698.2
2.9-3.016.90.1711701.67599.7
3.01-3.156.80.14712161.78199.8
3.15-3.326.80.13311912.04299.4
3.32-3.526.60.11611972.34898.9
3.52-3.86.40.10311972.62498.8
3.8-4.185.70.09111412.89294.5
4.18-4.786.60.09211972.99699
4.78-6.026.80.0912072.74498.8
6.02-506.40.06912212.77897.5

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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
Starting model: 2B1V

2b1v


Resolution: 2.22→46.701 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1906 8.39 %
Rwork0.2057 20823 -
obs0.2096 22729 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.41 Å2 / Biso mean: 57.6233 Å2 / Biso min: 24.51 Å2
Refinement stepCycle: final / Resolution: 2.22→46.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 54 91 3970
Biso mean--38.65 46.39 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033964
X-RAY DIFFRACTIONf_angle_d0.7665363
X-RAY DIFFRACTIONf_chiral_restr0.027632
X-RAY DIFFRACTIONf_plane_restr0.003664
X-RAY DIFFRACTIONf_dihedral_angle_d13.6671447
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 (%)
2.22-2.26410.3514990.31271089118870
2.2641-2.32530.33211350.26881363149886
2.3253-2.39380.30111210.26621491161291
2.3938-2.4710.29031250.24881480160594
2.471-2.55930.28331450.23891479162494
2.5593-2.66180.28011350.24121506164194
2.6618-2.78290.26211390.25481461160093
2.7829-2.92960.30241410.24131517165895
2.9296-3.11310.28991450.23431561170699
3.1131-3.35340.27491470.22951572171998
3.3534-3.69080.22331440.2071582172699
3.6908-4.22450.22761430.17621520166395
4.2245-5.32130.20251460.16561592173899
5.3213-46.7110.26091410.17671610175198
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)
15.0686-2.84530.52535.37231.18592.52120.5210.8340.3114-0.7431-0.5817-0.4435-0.4411-0.22060.08190.76280.09840.10230.61560.15540.331711.17157.2795-5.9536
25.0126-0.8841-2.18825.28661.27974.2426-0.11750.2410.1768-0.13550.0005-0.10940.04390.04150.10210.31510.00790.010.35260.03590.240316.0384.47471.2373
34.7843-1.63195.83320.5727-1.99137.05490.1741-0.3165-1.7220.04330.0246-0.85112.08270.72550.29421.17720.14540.10180.56380.05871.092818.8664-14.84137.7466
46.2125-1.1487-1.05215.136-0.54675.4950.12450.0238-0.05480.224-0.20910.26910.2857-0.24710.1210.55730.00910.12820.3911-0.00960.22995.8882.46826.1288
55.4527-0.2392-0.30042.26180.34363.14490.04790.10.13460.0071-0.0994-0.0629-0.1662-0.06130.10620.50220.02790.0370.3288-0.00190.22488.33676.66048.7966
64.93771.24725.18257.20062.47775.8785-0.33350.0746-0.010.20340.26490.96871.476-0.84380.09420.4979-0.0660.04140.90720.02410.5961-16.9461.705225.2867
71.02090.7874-2.29016.35090.81846.1232-0.3253-0.7152-0.17320.1680.5199-1.1463-0.87581.5608-0.04380.5483-0.01050.03860.9183-0.11450.58127.98110.669444.3393
83.0915-0.2419-0.54284.00721.59726.791-0.2134-0.3422-0.260.19590.02120.07920.35250.27560.20630.45490.05030.07220.39860.06080.28733.39953.51232.7917
94.7461.005-0.1423.68680.8776.72320.07770.12430.2006-0.18170.0483-0.3396-0.80360.2162-0.1310.5266-0.00980.10310.3459-0.01850.34255.044513.033226.2191
104.7701-3.3889-2.88685.23883.58782.6071-0.16571.03170.7496-2.46090.10720.80810.5290.2565-0.20251.50570.02720.05660.90410.07850.6785-0.6619-10.714115.2642
115.9085-1.97380.51622.8154-0.5525.28310.10430.20190.2295-0.2848-0.20790.116-0.0316-0.51720.09190.3809-0.00180.03950.3548-0.05470.2487-2.70017.546617.5495
122.7142-0.1203-2.26230.1995-0.15192.027-0.308-0.655-0.01540.4194-0.2524-0.5752-0.18490.78770.35910.92060.18030.02670.72430.19080.631614.7003-5.496633.5806
135.2967-3.2952-1.32172.44382.51739.01160.75830.57961.36390.0689-0.85811.2224-0.64071.40981.08420.6867-0.03460.27790.67660.1611.001825.69618.19541.3397
144.3004-3.2506-2.58686.12960.2162.6993-1.0316-0.5245-2.73280.3864-0.03270.84311.7713-0.6110.49580.9262-0.05260.02310.49390.08250.64651.1631-13.416634.9238
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 410 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 411 through 420 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 421 through 472 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 473 through 548 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 305 through 321 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 322 through 338 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 339 through 411 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 412 through 455 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 456 through 472 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 473 through 527 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 528 through 549 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 688 through 696 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 687 through 696 )D0

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