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

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Basic information

Entry
Database: PDB / ID: 5dyb
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-(3,4-dihydronaphthalen-2(1H)-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 / 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 / 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-5K2 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 24, 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)62,5906
Polymers61,9334
Non-polymers6572
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-29 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.154, 81.044, 58.100
Angle α, β, γ (deg.)90.000, 110.160, 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-5K2 / 4,4'-(3,4-dihydronaphthalen-2(1H)-ylidenemethanediyl)diphenol


Mass: 328.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
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: 2.27→50 Å / Num. obs: 21482 / % possible obs: 97.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.121 / Χ2: 0.97 / Net I/av σ(I): 17.879 / Net I/σ(I): 5.1 / Num. measured all: 146877
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.27-2.316.60.90710740.50698
2.31-2.356.80.82910710.50797.3
2.35-2.46.90.75610650.48197.8
2.4-2.456.90.63910800.49696.9
2.45-2.56.80.57910720.51298.2
2.5-2.566.70.51410770.54898.3
2.56-2.626.80.4310810.5898.5
2.62-2.696.70.36710880.58197.5
2.69-2.776.50.3110590.63997.1
2.77-2.866.40.2689890.68290
2.86-2.967.20.22310810.77699.1
2.96-3.087.10.19311050.83498.6
3.08-3.227.20.16410970.88999.4
3.22-3.397.10.13711141.12798.8
3.39-3.670.11410811.31398.9
3.6-3.886.70.09510801.66697.6
3.88-4.276.40.09210042.07390.8
4.27-4.897.10.08111061.78298.7
4.89-6.1670.07711021.47498.8
6.16-506.60.06310561.97692.1

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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: 2.27→45.248 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 1873 9.22 %
Rwork0.1782 18448 -
obs0.1837 20321 91.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.6 Å2 / Biso mean: 51.678 Å2 / Biso min: 14.52 Å2
Refinement stepCycle: final / Resolution: 2.27→45.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 50 121 3925
Biso mean--39.72 47.75 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043874
X-RAY DIFFRACTIONf_angle_d0.8115243
X-RAY DIFFRACTIONf_chiral_restr0.03621
X-RAY DIFFRACTIONf_plane_restr0.003648
X-RAY DIFFRACTIONf_dihedral_angle_d14.3361412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2577-2.31880.2691220.23531228135079
2.3188-2.3870.28471400.22681298143885
2.387-2.4640.24281340.22561366150087
2.464-2.55210.27341350.21771380151589
2.5521-2.65430.28711540.2141384153891
2.6543-2.77510.27361320.22761417154990
2.7751-2.92130.27981490.19741360150989
2.9213-3.10430.24091500.19211497164797
3.1043-3.34390.24241500.19541517166798
3.3439-3.68030.23221580.17631509166797
3.6803-4.21250.19221440.14671442158692
4.2125-5.3060.2131540.14551546170099
5.306-45.25730.24551510.16551504165594
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)
14.8696-0.71261.29082.14420.84793.4060.14360.36090.9084-0.6030.31810.7059-0.3876-0.8519-0.04830.46770.13910.00780.60270.14510.65051.96533.8829-5.0543
24.4534-1.25281.17972.394-0.73922.75370.33610.3346-0.68630.1655-0.069-0.78890.46140.0427-0.19020.4089-0.0795-0.05590.5302-0.07660.492420.52779.214-5.9133
34.3065-0.1335-1.11814.421.48833.6920.01570.12110.10520.11510.0963-0.335-0.14120.2407-0.13940.2267-0.0085-0.01930.32650.02280.240217.282123.03752.2589
44.42830.8208-2.57014.90991.08854.3991-0.2307-0.1055-1.22650.3895-0.17420.00031.03570.49920.21620.5630.01370.07860.3375-0.00290.566714.83913.92191.296
54.8223-0.205-1.05894.87861.13812.8112-0.05450.2038-0.32830.3739-0.01490.27580.2987-0.15830.14830.2611-0.0030.03870.22030.03530.22475.272117.12065.5137
64.86590.3379-0.39812.74170.54871.82810.0237-0.08080.10860.1271-0.1226-0.10830.16940.07740.07890.32280.01970.03220.24760.00670.18148.856221.17598.3694
73.76251.69165.62022.84451.66978.64680.3313-0.2668-0.63020.11410.0750.02390.1367-0.4387-0.27780.30010.05150.07680.4604-0.06550.3957-3.181521.11635.5635
83.2272-0.4947-0.22863.85780.75244.5813-0.0558-0.215-0.36090.01650.04440.06640.26050.08340.06940.32540.01830.03020.29870.03160.24463.098314.041731.6329
91.8253-0.1642-0.16936.4691-1.97145.1080.2506-0.54380.49950.05450.0544-0.8017-0.94690.41230.01440.586-0.08250.03330.4752-0.07860.41829.353332.037435.4687
107.7597-0.70722.02865.7748-0.12735.9227-0.43250.45760.90720.2053-0.0653-0.5899-1.20730.4180.1350.5765-0.07710.01810.28880.02080.38428.075632.182124.4795
112.02270.09890.31745.10870.11354.30470.2620.22030.0052-0.4971-0.4435-0.10520.3562-0.28360.02990.38270.01880.0160.41680.00230.2343-3.295417.373321.3573
123.1736-0.66860.88182.3061-0.81195.1055-0.03310.031-0.0622-0.1312-0.01040.13320.108-0.42450.04280.3101-0.03860.06860.3181-0.05380.2574-1.279521.547618.2738
135.4568-0.0422-0.57073.9901-1.21317.22430.8271-0.0253-0.21970.0456-0.2963-1.12431.16560.704-0.03860.72540.1494-0.01680.4491-0.01930.823115.4539.74233.7599
147.7925-0.3386-4.45731.28612.55226.97060.1588-0.86630.3114-0.39940.262-0.6044-1.16920.342-0.42510.3359-0.06250.04020.4571-0.02610.642125.992133.49141.452
152.81732.6760.99057.17540.33357.1849-0.96-1.149-2.3871-0.230.1888-0.72951.6971-0.47310.52030.819-0.0173-0.0240.50180.18750.63312.20021.67335.2588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 322 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 323 through 338 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 395 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 396 through 421 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 422 through 473 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 474 through 548 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 305 through 338 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 339 through 393 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 394 through 421 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 422 through 438 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 439 through 470 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 471 through 530 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 531 through 548 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 687 through 696 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 688 through 696 )D0

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