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- PDB-5dlr: Crystal Structure of the ER-alpha Ligand-binding Domain in comple... -

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Basic information

Entry
Database: PDB / ID: 5dlr
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in complex with a triaryl-ethylene compound 4,4'-(2-phenylethene-1,1-diyl)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
4,4'-(2-phenylethene-1,1-diyl)diphenol / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 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 7, 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)62,5106
Polymers61,9334
Non-polymers5772
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-29 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.824, 81.803, 58.351
Angle α, β, γ (deg.)90.000, 110.580, 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 / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-5DJ / 4,4'-(2-phenylethene-1,1-diyl)diphenol


Mass: 288.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 38.6 %
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: Mar 21, 2011
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: 2.26→50 Å / Num. obs: 22661 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.92 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.978 / Net I/av σ(I): 28.518 / Net I/σ(I): 11.9 / Num. measured all: 85666
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.26-2.33.80.43611411.191100
2.3-2.343.80.34211161.251100
2.34-2.393.80.33911421.225100
2.39-2.433.80.26610981.262100
2.43-2.493.80.25111471.279100
2.49-2.553.80.21811141.277100
2.55-2.613.80.19611301.338100
2.61-2.683.80.16711231.274100
2.68-2.763.80.14911281.451100
2.76-2.853.80.13211271.477100
2.85-2.953.80.10311371.582100
2.95-3.073.80.09111391.682100
3.07-3.213.80.0811181.907100
3.21-3.383.80.07111352.072100
3.38-3.593.80.06711462.462100
3.59-3.863.80.06111282.884100
3.86-4.253.80.06211373.24999.9
4.25-4.873.80.06211363.43100
4.87-6.133.80.06511543.327100
6.13-503.60.05811654.01199.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.26→40.376 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1937 8.87 %
Rwork0.1817 19892 -
obs0.1861 21829 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.96 Å2 / Biso mean: 49.395 Å2 / Biso min: 16.43 Å2
Refinement stepCycle: final / Resolution: 2.26→40.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3895 0 44 136 4075
Biso mean--32.64 43.36 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034014
X-RAY DIFFRACTIONf_angle_d0.7665422
X-RAY DIFFRACTIONf_chiral_restr0.055637
X-RAY DIFFRACTIONf_plane_restr0.003673
X-RAY DIFFRACTIONf_dihedral_angle_d15.371504
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 (%)
2.2547-2.31110.28041030.2321120122376
2.3111-2.37360.26631460.22251355150192
2.3736-2.44340.31771350.21371411154695
2.4434-2.52230.27631300.20881389151993
2.5223-2.61240.25471340.2081418155295
2.6124-2.7170.24291420.20821390153296
2.717-2.84060.26991380.20871438157698
2.8406-2.99030.29271450.19811458160398
2.9903-3.17760.2411530.20281462161598
3.1776-3.42290.23911330.18911492162599
3.4229-3.76710.21511430.17381438158199
3.7671-4.31160.20311480.151414971645100
4.3116-5.43010.19951450.151915031648100
5.4301-40.38260.2121420.17671521166399
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)
10.9661-0.4956-0.54752.4896-0.22144.22660.0329-0.1635-0.0340.3010.0829-0.0854-0.0218-0.0635-0.20620.2710.06780.04270.3253-0.06810.3429-18.612320.92878.5913
21.7944-1.6126-0.54524.31081.19143.8626-0.1122-0.102-0.30210.1359-0.05390.270.4353-0.0580.17840.3366-0.0280.06570.27330.01390.2819-15.043213.39514.0305
31.3083-0.15072.50165.9704-0.656.94580.1663-0.36010.30480.3261-0.0128-0.672-1.00510.7893-0.22570.4142-0.0969-0.00830.5018-0.03030.4073-7.13231.71538.0222
42.88320.3989-0.3234.24390.1224.39340.05510.05840.0887-0.2514-0.0845-0.2191-0.26240.09450.04790.30140.00850.02490.29990.02190.202-14.81422.5637-4.4193
53.5398-0.22130.65430.9911-1.71994.91170.0275-0.0531-0.4761-0.3685-0.02970.6860.5146-0.73950.07120.2461-0.05640.00430.4512-0.05310.3453-28.298817.3246-10.9883
64.7422-1.2221.70842.815-0.59874.63860.0837-0.07050.0017-0.1713-0.1512-0.28780.04590.29270.06830.3144-0.02880.05950.241-0.00520.2727-10.216322.0262-7.0031
76.7412.363-0.16863.84380.30495.88070.1304-0.2464-0.7301-0.0014-0.1355-0.75090.331.5682-0.11280.4670.07430.03040.60830.13540.7177-1.60078.50195.3339
82.20551.8654-1.01358.354-1.55422.15810.78650.76481.1319-0.5748-0.56620.3491-0.591-0.715-0.21540.50250.17540.0640.52850.07630.4995-15.079333.6708-32.1277
94.5279-0.0537-0.12394.15980.44711.75030.5070.6382-1.0208-1.0507-0.6659-0.36290.50820.39640.07560.44360.07070.03480.5363-0.01050.46794.34737.2493-33.7243
103.3007-0.5786-0.85333.80961.36924.0674-0.08620.07350.09130.01230.0729-0.22810.10260.11820.03330.23010.01850.00850.26520.03040.226-0.90318.6462-26.1789
114.2880.24414.0560.2110.3263.9732-0.07210.2552-0.0769-0.19860.004-1.36041.11081.13080.33360.89810.01830.08460.59290.11120.81412.4098-0.2245-18.5526
125.338-0.3775-0.36825.379-0.13823.7017-0.11210.0207-0.20330.0053-0.01840.22380.3229-0.210.14040.25980.0130.05820.2631-0.00430.184-11.706816.1613-21.7745
137.61640.13910.18084.0354-0.18283.92620.2022-0.05930.9515-0.4247-0.63860.0549-0.3872-0.39330.20160.38840.1111-0.01430.40780.01920.4308-20.674129.7547-23.7195
147.2085-1.00280.74622.5223-0.35922.4430.3127-0.0288-0.03570.1192-0.3052-0.13270.35110.11450.030.3838-0.0152-0.00970.2631-0.00770.2232-9.009516.2148-15.8046
155.0867-0.9052-1.24237.16510.87115.27460.0411-0.47630.40870.21930.1383-1.32580.70440.8223-0.08730.35250.0688-0.04560.43380.02720.53511.421619.389-18.6908
162.0030.05997.57917.99360.37235.6723-0.5269-1.7896-2.3414-0.01490.4293-0.50871.4523-0.74750.04380.71530.03630.10590.42910.15070.7623-15.42910.77298.032
172.44392.33240.39237.50432.90933.16340.6472-0.31811.2772-0.80860.2626-0.4003-1.4080.9079-0.96350.4212-0.06370.14660.49490.03270.7049.149132.7141-25.7707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 341 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 394 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 395 through 419 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 420 through 468 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 469 through 496 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 497 through 531 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 532 through 550 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 304 through 322 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 323 through 338 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 411 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 412 through 421 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 422 through 472 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 473 through 496 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 497 through 531 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 532 through 548 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 687 through 696 )C0
17X-RAY DIFFRACTION17chain 'D' and (resid 687 through 696 )D0

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