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

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Basic information

Entry
Database: PDB / ID: 5dxq
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-[(1s,5s)-bicyclo[3.3.1]non-9-ylidenemethanediyl]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 / 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 / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina 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 / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / 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 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / 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-5HZ / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Sep 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)62,5746
Polymers61,9334
Non-polymers6412
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-27 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.910, 81.070, 58.340
Angle α, β, γ (deg.)90.00, 111.09, 90.00
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-5HZ / 4,4'-[(1s,5s)-bicyclo[3.3.1]non-9-ylidenemethanediyl]diphenol


Mass: 320.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.93 Å3/Da / Density % sol: 36.14 %
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 26, 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: 2.37→50 Å / Num. obs: 18779 / % possible obs: 98.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 27.19 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.114 / Net I/av σ(I): 16.36 / Net I/σ(I): 4.6 / Num. measured all: 115105
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.37-2.415.70.8039130.50798.7
2.41-2.455.90.7029560.599.3
2.45-2.56.10.6259250.5299
2.5-2.556.10.6029730.52799.5
2.55-2.616.10.4978980.56998.8
2.61-2.676.20.4349500.61799
2.67-2.745.80.3829020.66897.6
2.74-2.815.30.3359240.66295.4
2.81-2.896.20.299410.70998.6
2.89-2.996.60.2459330.78699.6
2.99-3.096.50.2189520.87499.3
3.09-3.226.50.1969580.89799.5
3.22-3.366.40.1649400.98299.1
3.36-3.546.40.149451.23599.1
3.54-3.766.20.1219371.44198.8
3.76-4.055.70.1089211.77996.2
4.05-4.466.20.1039411.95698
4.46-5.16.50.1029442.09399.2
5.1-6.436.40.0999671.84598.8
6.43-505.80.0789592.95497.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B1V

2b1v


Resolution: 2.4→45.191 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2393 1582 10.1 %
Rwork0.1937 --
obs0.1982 15667 84.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3701 0 48 102 3851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023852
X-RAY DIFFRACTIONf_angle_d0.5425223
X-RAY DIFFRACTIONf_dihedral_angle_d12.2771389
X-RAY DIFFRACTIONf_chiral_restr0.02627
X-RAY DIFFRACTIONf_plane_restr0.002645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.3362750.2289576X-RAY DIFFRACTION39
2.4775-2.5660.2822990.2348874X-RAY DIFFRACTION57
2.566-2.66880.30651300.23921096X-RAY DIFFRACTION75
2.6688-2.79020.24341410.24021317X-RAY DIFFRACTION86
2.7902-2.93730.28081590.22621385X-RAY DIFFRACTION94
2.9373-3.12130.28051480.22481452X-RAY DIFFRACTION96
3.1213-3.36220.27961600.21131465X-RAY DIFFRACTION97
3.3622-3.70040.21591750.18531463X-RAY DIFFRACTION98
3.7004-4.23550.2011580.16191463X-RAY DIFFRACTION96
4.2355-5.3350.21331730.1621490X-RAY DIFFRACTION99
5.335-45.19890.21371640.181504X-RAY DIFFRACTION98
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)
11.2225-0.42160.62461.5593-0.10060.32730.0394-0.00030.0493-0.20960.0750.4044-0.19-0.38630.11680.53670.6013-0.1080.91790.26320.38050.678217.2815-5.9294
22.67861.32420.12772.4166-1.01733.92190.04440.0111-0.5387-0.4812-0.3614-0.2920.19290.23630.30930.23720.08930.06120.32240.07360.213619.8168-3.0719-6.9225
35.7508-0.6136-0.04652.46021.38153.91470.05130.3208-0.1233-0.12440.1958-0.1809-0.04530.2087-0.18210.12930.01790.00590.23010.02670.117521.13623.0856-0.8836
44.33070.6630.16443.35640.40874.01680.17150.32820.60520.0789-0.04580.0751-0.678-0.3589-0.10440.21130.04420.06420.24570.02360.143813.640612.19624.7029
54.45072.2744-0.93921.9320.43431.9745-0.32210.6438-0.80530.037-0.2350.3380.913-0.73820.37890.4524-0.16130.07010.3482-0.11720.306311.8436-9.4188-2.9124
61.33151.3614-0.79324.93023.02354.629-0.1103-0.1386-0.74530.97610.1401-0.87790.63910.5276-0.15551.1910.25370.04040.29720.02720.616920.1958-13.63728.556
72.2821-0.4695-0.24993.32730.65173.34180.02080.4285-0.23630.1294-0.36350.27180.5016-1.03820.20920.1929-0.04320.03940.4736-0.0310.1564.2497-0.00783.9549
83.5916-2.2545-0.65993.66935.0439.68750.2286-0.96351.54161.7439-0.15950.0401-0.8281-0.67140.07160.74980.07810.04370.4758-0.16850.56389.944917.35514.7961
93.7107-0.02271.56090.302-0.04321.75720.06470.74440.4745-0.3481-0.28760.2651-0.4257-0.44720.28250.23160.433-0.0310.95690.19860.3791-4.560414.65593.1924
102.38370.1858-0.98972.26160.2742.8883-0.1269-0.061-0.04660.2165-0.0241-0.23020.19080.00760.13760.2198-0.0044-0.04480.23190.01350.123913.06562.886610.5836
115.5825-1.69590.73262.5897-0.39085.16110.04880.7828-0.8862-0.25930.29850.79990.4172-1.2206-0.1880.1865-0.09780.00790.93920.02730.5348-16.85981.045725.8925
120.6501-1.3052-1.09293.57260.77214.0107-0.1631-0.0980.12310.36430.5636-0.8863-0.30151.1437-0.30460.36210.0698-0.0340.5222-0.17730.33857.549810.753843.7628
133.0011-1.592-0.91723.67830.19554.624-0.2349-0.1779-0.4641-0.07230.04560.24870.80730.02690.06920.3612-0.00070.05110.19590.02680.13682.2132-0.703631.5601
142.69010.129-1.06335.04730.16966.22590.0664-0.24840.41290.16340.2273-0.5504-1.10640.5761-0.02060.4065-0.15310.05390.2652-0.07470.298.648716.911630.4663
154.09480.36780.98962.1266-0.86484.96350.06390.2147-0.1375-0.0756-0.11990.1630.0999-1.235-0.06930.1814-0.00330.03050.4962-0.04060.1549-8.54484.827118.9772
163.6121-0.8668-0.17883.4552-0.90614.6804-0.1247-0.0867-0.09270.18260.0482-0.31560.08550.26440.17050.15980.01540.06170.185-0.05010.12728.18593.920423.903
172.5133-0.5978-1.25882.7582-0.24851.378-0.15450.06020.1464-0.0656-0.3261-0.1459-0.21740.30440.34380.3363-0.09320.18540.35450.01370.752425.23118.08211.4066
180.39790.22590.77470.32770.51931.53440.0155-0.6777-0.97591.0438-0.280.28720.4891-0.23780.08890.9002-0.12480.19470.12970.14920.6437-0.098-12.854236.2965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 306 through 322 )
2X-RAY DIFFRACTION2chain 'A' and (resid 323 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 363 )
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 394 )
5X-RAY DIFFRACTION5chain 'A' and (resid 395 through 411 )
6X-RAY DIFFRACTION6chain 'A' and (resid 412 through 421 )
7X-RAY DIFFRACTION7chain 'A' and (resid 422 through 455 )
8X-RAY DIFFRACTION8chain 'A' and (resid 456 through 472 )
9X-RAY DIFFRACTION9chain 'A' and (resid 473 through 496 )
10X-RAY DIFFRACTION10chain 'A' and (resid 497 through 548 )
11X-RAY DIFFRACTION11chain 'B' and (resid 304 through 322 )
12X-RAY DIFFRACTION12chain 'B' and (resid 323 through 338 )
13X-RAY DIFFRACTION13chain 'B' and (resid 339 through 394 )
14X-RAY DIFFRACTION14chain 'B' and (resid 395 through 438 )
15X-RAY DIFFRACTION15chain 'B' and (resid 439 through 496 )
16X-RAY DIFFRACTION16chain 'B' and (resid 497 through 548 )
17X-RAY DIFFRACTION17chain 'C' and (resid 687 through 696 )
18X-RAY DIFFRACTION18chain 'D' and (resid 688 through 697 )

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