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

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Basic information

Entry
Database: PDB / ID: 5dke
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in complex with a 3-naphthyl-substituted, methyl, cis-diaryl-ethylene compound 4,4'-[2-(naphthalen-2-yl)prop-1-ene-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 / 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
Chem-5C8 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords

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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)62,6386
Polymers61,9334
Non-polymers7052
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-29 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.758, 77.301, 57.528
Angle α, β, γ (deg.)90.000, 109.790, 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*PLUS
#3: Chemical ChemComp-5C8 / 4,4'-[2-(naphthalen-2-yl)prop-1-ene-1,1-diyl]diphenol


Mass: 352.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H20O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.85 Å3/Da / Density % sol: 33.42 %
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: 2.6→50 Å / Num. obs: 13294 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.156 / Χ2: 0.902 / Net I/av σ(I): 11.806 / Net I/σ(I): 4.2 / Num. measured all: 79462
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.645.90.8986780.53699.6
2.64-2.695.80.6846360.54698.6
2.69-2.745.60.7226860.55696.8
2.74-2.85.20.6226000.57492.3
2.8-2.865.60.5346460.58194.9
2.86-2.936.20.4576730.594100
2.93-36.30.3926710.5899.9
3-3.086.20.3536620.64199.5
3.08-3.176.20.2986780.65599.6
3.17-3.286.20.2836600.77199.1
3.28-3.396.10.2196870.81799.3
3.39-3.536.10.1896750.86599
3.53-3.696.10.1636501.01799.1
3.69-3.885.90.1416671.08997.4
3.88-4.135.20.136361.32493.1
4.13-4.456.10.1186671.22898.7
4.45-4.896.40.16801.20899.1
4.89-5.66.40.1016731.06899.6
5.6-7.0560.1016831.07498.6
7.05-505.60.0766862.34396.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.6→44.943 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 1242 9.97 %
Rwork0.2153 11221 -
obs0.22 12463 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.42 Å2 / Biso mean: 48.2758 Å2 / Biso min: 10.83 Å2
Refinement stepCycle: final / Resolution: 2.6→44.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 54 60 3810
Biso mean--23.39 38.63 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023830
X-RAY DIFFRACTIONf_angle_d0.5915187
X-RAY DIFFRACTIONf_chiral_restr0.022618
X-RAY DIFFRACTIONf_plane_restr0.002640
X-RAY DIFFRACTIONf_dihedral_angle_d13.131406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5904-2.69410.31661230.2741087121081
2.6941-2.81670.32711200.2761127124783
2.8167-2.96520.33661350.25351209134489
2.9652-3.15090.30071460.24631259140593
3.1509-3.39410.29611390.23091278141794
3.3941-3.73550.25891410.20571304144595
3.7355-4.27570.26781380.19221249138792
4.2757-5.38550.22991520.18751348150099
5.3855-44.94980.21881480.20751360150896
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)
15.1045-2.6853-0.03373.82120.11692.70130.15861.1250.7175-0.2481-0.6158-0.19650.15490.28730.5080.34820.00840.0430.48580.09870.36898.01623.2818-4.0429
22.1913-1.1665-1.56943.32180.42292.7438-0.12120.54480.07980.0513-0.0839-0.1659-0.06450.32550.04190.3364-0.0589-0.04430.5053-0.01290.302218.399521.84891.0348
34.12650.7520.32585.10840.74961.76490.0920.0723-0.25830.131-0.1454-0.26180.17720.120.05840.2619-0.01220.01330.34670.02370.20715.478210.94445.4462
48.9408-5.22464.43654.1577-1.54894.3471-0.03830.0608-1.12150.34180.13840.5635-0.2924-0.18880.38750.451-0.02570.00510.2952-0.02580.50468.44834.48369.1997
55.8431-0.0178-2.02874.50220.14591.9962-0.00340.10990.1772-0.2919-0.13250.1409-0.2068-0.12880.07240.28720.0208-0.01140.27830.00940.25480.091423.89545.497
62.7901-2.37840.19762.0388-0.78672.9876-0.5347-0.3415-0.08760.19650.28350.0427-0.05120.11540.29830.358-0.01550.01730.2728-0.01370.20967.263714.366713.7125
76.50290.59290.68649.0596-3.57258.5182-0.6408-0.6020.16670.41780.0986-1.1501-0.16310.65320.4330.3876-0.0255-0.08540.66640.06580.506928.81817.178711.3197
83.8941.39731.01442.4627-0.09042.76510.2466-0.94230.09850.4345-0.33480.11220.1873-0.27660.07230.4425-0.0570.13870.74510.0040.4524-1.044918.775537.9904
93.23690.8611.99752.68430.20284.72150.0085-0.3116-0.38170.2259-0.0258-0.05580.5816-0.13020.11190.43470.00480.0580.32670.03040.28973.291611.073333.2032
102.8856-0.14910.09516.02860.66784.60980.03430.14610.3467-0.1793-0.2357-0.1061-0.43180.45850.60550.561-0.0614-0.0690.41870.00260.376912.407629.105236.7879
112.0646-2.12182.45945.060.01625.2521-0.1738-0.45810.3817-0.58960.37-0.0693-0.71780.1122-0.23590.5481-0.1851-0.09870.43230.06810.46619.814828.690726.6818
122.1172-0.6891.68862.51250.00133.85840.11920.0312-0.0455-0.03980.0630.04810.2249-0.4795-0.10060.2717-0.04160.05920.4605-0.00190.3829-7.561217.198821.5991
132.5141-1.73772.17862.1834-1.75143.848-0.26760.2451-0.07370.2555-0.02980.0206-0.30330.39630.26430.2937-0.01760.10140.4638-0.08650.3294.135721.673119.5944
149.78683.6859-3.52883.2074-3.45983.74990.32670.0032-0.99460.81630.2231-0.64120.41710.7915-0.07040.58910.2082-0.15680.5307-0.03290.813616.52987.282134.8002
153.94652.91880.74662.6691-0.26762.34540.51772.41140.2302-0.1042-0.19390.5803-0.164-0.4197-0.14031.53340.21780.23321.7442-0.16130.594421.31754.359422.7378
167.7153-0.56581.0986.1131.15348.3636-0.5814-0.0804-0.4252-0.91220.70190.0796-1.63120.2904-0.55210.67860.05240.1450.4903-0.0150.472625.972631.29583.1261
175.80313.22492.89385.9705-1.50833.7624-0.67170.5776-0.0709-0.44590.64821.1286-0.22380.4029-0.17330.8993-0.2084-0.00730.49240.04190.78612.804-0.894937.9577
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 371 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 372 through 420 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 421 through 438 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 439 through 496 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 497 through 530 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 531 through 548 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 305 through 341 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 342 through 394 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 395 through 420 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 421 through 438 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 439 through 496 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 497 through 525 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 526 through 547 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 548 through 555 )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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