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

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Basic information

Entry
Database: PDB / ID: 5drm
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in complex with a dichloro-substituted, 2,5-diarylthiophene-core ligand 4,4'-thiene-2,5-diylbis(3-chlorophenol)
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
4,4'-thiene-2,5-diylbis(3-chlorophenol) / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.241 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 16, 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)62,6076
Polymers61,9334
Non-polymers6742
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-32 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.106, 84.502, 58.737
Angle α, β, γ (deg.)90.00, 108.38, 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 / 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 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-5ET / 4,4'-thiene-2,5-diylbis(3-chlorophenol)


Mass: 337.220 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10Cl2O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.51 %
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: Jan 14, 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: 2.241→46.529 Å / Num. obs: 24971 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.2
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / % possible all: 95.88

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QA8

2qa8


Resolution: 2.241→46.529 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 1936 8.04 %
Rwork0.1822 --
obs0.1848 24084 96.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.241→46.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 0 42 253 4144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024024
X-RAY DIFFRACTIONf_angle_d0.5485454
X-RAY DIFFRACTIONf_dihedral_angle_d12.4041466
X-RAY DIFFRACTIONf_chiral_restr0.022644
X-RAY DIFFRACTIONf_plane_restr0.003679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2405-2.29660.2781180.23651385X-RAY DIFFRACTION85
2.2966-2.35870.25091400.22031486X-RAY DIFFRACTION91
2.3587-2.42810.24921270.20881509X-RAY DIFFRACTION92
2.4281-2.50640.24951270.20081536X-RAY DIFFRACTION93
2.5064-2.5960.23841400.19941558X-RAY DIFFRACTION95
2.596-2.69990.26071440.20831585X-RAY DIFFRACTION97
2.6999-2.82280.27111400.19931593X-RAY DIFFRACTION97
2.8228-2.97160.21051290.19251603X-RAY DIFFRACTION98
2.9716-3.15770.21261490.19451609X-RAY DIFFRACTION98
3.1577-3.40150.20451420.18811635X-RAY DIFFRACTION99
3.4015-3.74370.20191430.16481660X-RAY DIFFRACTION100
3.7437-4.2850.19181470.14831642X-RAY DIFFRACTION100
4.285-5.39740.17451430.15611662X-RAY DIFFRACTION100
5.3974-46.53940.21321470.18551685X-RAY DIFFRACTION100
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)
14.82841.8924-0.63473.4307-0.07513.04370.0117-0.33170.6720.03180.1637-0.4502-0.18950.3787-0.14070.3738-0.0651-0.06870.4821-0.11760.411518.038310.269631.7948
21.51961.3796-0.20463.1820.11191.58350.1061-0.44520.11270.4076-0.28280.77910.48880.10460.01680.31170.01350.04790.31750.04680.2991-9.03-8.543631.9133
31.76760.514-0.01282.6401-0.741.83540.0761-0.07090.13930.14670.02780.1827-0.1499-0.0661-0.11120.14020.02470.03040.16910.00870.1546-0.56624.87424.4497
42.53830.1938-1.38844.1151-0.14953.1069-0.17450.0149-0.38960.0149-0.09110.03430.582-0.03890.06910.27190.00140.06260.19990.04030.2987-3.1518-14.531223.9621
57.12360.98940.5983.0580.09732.9311-0.15980.1694-0.6592-0.11890.115-0.13770.2875-0.05210.08780.2430.00770.03650.1421-0.00130.22274.4479-12.365917.5638
62.2195-1.0831-0.52114.1344-0.46931.84490.0591-0.2934-0.19610.3050.0562-0.1110.07860.32030.01490.1580.00430.00140.244-0.01130.193213.2844-0.581224.0575
71.75181.5017-1.02215.3633-5.31675.84230.05021.10590.5697-1.26820.6225-1.1628-0.80750.0861-0.03090.4770.05110.14110.50510.04320.5718.996517.577312.7834
83.57020.687-1.03061.878-0.32530.6106-0.1173-0.06150.1322-0.02510.0937-0.0375-0.04420.02480.03960.1650.0117-0.00640.18190.01410.131812.62340.831817.1765
92.62711.14550.46872.23450.69941.23920.11760.46090.2821-0.32110.28940.6851-0.0935-0.55690.00180.2350.0043-0.08750.2749-0.02120.4812-12.27355.356418.2559
103.98130.5351.48692.57540.91423.70440.06520.4492-0.4401-0.35970.0872-0.0337-0.13090.5256-0.16910.2661-0.02490.10180.2841-0.02410.236821.0749-1.7384-7.7285
114.5511-1.26871.44944.1967-0.52594.40850.04390.19650.0522-0.83350.16620.06170.1858-0.3424-0.00330.3228-0.01840.00960.2450.03040.16579.4918-2.2361-11.8082
123.503-0.07510.78612.31660.89433.45190.00270.0259-0.50060.39320.00250.09940.4082-0.0174-0.04740.28270.00170.01040.2080.01530.151512.4255-7.072-2.1751
131.06291.01030.4912.49830.40276.301-0.04490.05040.5017-0.64670.03850.3271-1.0818-0.8231-0.02670.69760.1518-0.00920.29610.06410.30816.784414.7562-8.3619
143.1008-0.3490.31613.04490.02792.5151-0.0496-0.06670.3149-0.0417-0.04190.0047-0.35720.00690.04210.2684-0.01290.00980.18210.02860.15815.15617.22311.8837
151.1372-2.28390.38437.5738-2.4321.9416-0.0807-0.1868-0.90740.18320.04720.20350.5596-0.0944-0.01360.5311-0.10330.07090.91730.07890.65639.4648-15.27899.1436
163.6115-0.20960.60122.37270.19322.6997-0.00160.1012-0.1726-0.01930.0059-0.11450.13920.01470.00990.18850.0070.05440.19470.03850.14417.692-1.13197.9316
178.449-5.77842.744.1905-1.8651.1239-0.26130.77820.1358-0.00070.06440.3659-0.0013-1.11850.1350.4714-0.036-0.0810.5550.02890.4703-2.7259-6.1117-8.8606
180.16650.0671-0.25480.04630.11191.95590.1676-0.18960.5275-0.03220.06140.0405-0.59950.24220.20960.2552-0.04470.05760.21120.01750.3878-6.394617.295226.1643
190.0248-0.0039-0.00540.04040.04530.01920.30590.2608-0.45120.0228-0.28910.07380.6193-0.098700.4873-0.0387-0.02010.3553-0.05710.30378.224-16.6248-11.3559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 394 )
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 420 )
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 437 )
6X-RAY DIFFRACTION6chain 'A' and (resid 438 through 455 )
7X-RAY DIFFRACTION7chain 'A' and (resid 456 through 471 )
8X-RAY DIFFRACTION8chain 'A' and (resid 472 through 531 )
9X-RAY DIFFRACTION9chain 'A' and (resid 532 through 548 )
10X-RAY DIFFRACTION10chain 'B' and (resid 305 through 340 )
11X-RAY DIFFRACTION11chain 'B' and (resid 341 through 363 )
12X-RAY DIFFRACTION12chain 'B' and (resid 364 through 394 )
13X-RAY DIFFRACTION13chain 'B' and (resid 395 through 420 )
14X-RAY DIFFRACTION14chain 'B' and (resid 421 through 455 )
15X-RAY DIFFRACTION15chain 'B' and (resid 456 through 465 )
16X-RAY DIFFRACTION16chain 'B' and (resid 466 through 527 )
17X-RAY DIFFRACTION17chain 'B' and (resid 528 through 548 )
18X-RAY DIFFRACTION18chain 'C' and (resid 687 through 696 )
19X-RAY DIFFRACTION19chain 'D' and (resid 688 through 696 )

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