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

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Basic information

Entry
Database: PDB / ID: 5dkb
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in complex with a 3-methylphenylamino-substituted ethyl triaryl-ethylene derivative 4,4'-(2-{3-[(3-methylphenyl)amino]phenyl}but-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 / 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-5C9 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 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)63,1987
Polymers61,9334
Non-polymers1,2653
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-28 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.347, 82.844, 58.458
Angle α, β, γ (deg.)90.000, 111.320, 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-5C9 / 4,4'-(2-{3-[(3-methylphenyl)amino]phenyl}but-1-ene-1,1-diyl)diphenol


Mass: 421.530 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H27NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
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: 2.19→50 Å / Num. obs: 25440 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.057 / Χ2: 0.475 / Net I/av σ(I): 22.571 / Net I/σ(I): 6 / Num. measured all: 175970
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.19-2.236.80.66312570.45899.5
2.23-2.2770.512730.45999.5
2.27-2.3170.4712850.46199.9
2.31-2.3670.39212660.45599.9
2.36-2.416.90.37412830.45699.8
2.41-2.4770.30712700.45399.8
2.47-2.5370.25912750.45499.9
2.53-2.66.90.22312770.47199.4
2.6-2.676.80.19812830.4799.1
2.67-2.766.50.15212410.46398.5
2.76-2.866.30.13812300.49294.7
2.86-2.977.20.112700.47499.6
2.97-3.117.20.08112690.47799.6
3.11-3.277.10.06712990.49199.6
3.27-3.487.10.0512620.48899.5
3.48-3.746.90.04212840.49998.8
3.74-4.126.30.03412340.50796.1
4.12-4.727.10.03312760.54299.2
4.72-5.947.10.03313020.5199.2
5.94-506.70.0213040.4298

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.4→47.364 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1495 7.94 %
Rwork0.1834 17324 -
obs0.1868 18819 95.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.69 Å2 / Biso mean: 54.7762 Å2 / Biso min: 16.84 Å2
Refinement stepCycle: final / Resolution: 2.4→47.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 96 109 3975
Biso mean--40.16 42.95 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033956
X-RAY DIFFRACTIONf_angle_d0.725351
X-RAY DIFFRACTIONf_chiral_restr0.05622
X-RAY DIFFRACTIONf_plane_restr0.002661
X-RAY DIFFRACTIONf_dihedral_angle_d15.2661489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.47750.28451390.21991482162190
2.4775-2.5660.30591170.21351539165693
2.566-2.66870.23931250.19751506163192
2.6687-2.79020.23681360.20691513164993
2.7902-2.93730.28121360.20561560169694
2.9373-3.12130.24751370.19311593173098
3.1213-3.36220.23031380.18841615175398
3.3622-3.70040.23531420.18111624176699
3.7004-4.23560.17991390.15711591173096
4.2356-5.33520.19341380.160816571795100
5.3352-47.37350.23361480.19241644179298
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)
11.95870.8419-2.05647.0436-2.09152.39790.7501-0.89110.80630.9754-0.9354-0.4674-0.88291.1283-0.06590.8207-0.3529-0.06570.5247-0.09340.4471-1.3876-5.06855.1828
22.45442.3572.15894.49472.6932.2874-0.1316-0.3792-1.0309-0.1597-0.3798-0.21621.1372-1.10830.41560.9298-0.30240.26730.7655-0.05910.6817-21.6196-30.3636.5043
34.09220.8578-2.03044.4624-1.32944.37670.1284-0.02360.36180.15040.0330.2397-0.0268-0.3055-0.0790.2985-0.00290.02010.2316-0.01140.2362-15.7936-18.548-1.1194
43.45220.4931-0.83394.4564-0.72053.6131-0.1046-0.0568-0.6050.045-0.0697-0.08940.85410.15960.1580.5166-0.01290.07250.25620.00480.2319-8.0798-27.66-4.2256
58.59834.963-1.07814.7875-1.30061.89080.08241.25351.0725-1.27841.0318-0.2813-0.964-0.3222-0.88920.90150.06050.13390.85460.09040.697-10.5163-5.8756-15.1954
65.34911.31420.0992.32330.15024.96460.288-0.3016-0.05570.1747-0.2982-0.211-0.07530.44470.07070.3608-0.01070.01680.26650.02390.1834-1.441-15.8339-8.162
72.48581.8963-0.5082.3721.12515.42110.3550.8254-0.7406-0.0928-0.45121.3590.302-2.27490.31560.6705-0.0356-0.00080.8114-0.05840.6592-27.6348-17.6681-9.369
84.84610.6312-0.18853.5128-0.82685.00920.17680.7184-0.6008-0.48690.1215-0.1417-0.0830.8554-0.11960.24380.04310.1440.49150.06050.30933.9871-17.4441-35.3236
92.3647-1.2676-0.20426.8342-0.7517.1067-0.4270.7896-0.2761-0.50370.27270.15330.8686-0.45160.06230.4685-0.10930.08580.38980.01070.2685-5.4074-22.4011-37.3175
102.9928-1.1939-0.25624.4011-0.67824.6808-0.22110.1338-0.25130.16830.0195-0.12050.43890.13370.12520.4373-0.01410.06080.2197-0.00340.2274-1.5193-20.4236-29.2904
112.3206-0.7012-2.56784.6823.16084.0867-0.50710.04430.09730.29610.42411.7619-0.8357-1.7332-0.75890.41160.42220.11731.49080.53650.7303-17.1864-7.6856-34.7743
126.2996-0.93180.43585.3752-1.47517.3298-0.13840.02930.31610.31840.10860.2157-0.67790.0771-0.02750.33870.00720.00410.24760.02880.1772-1.2542-11.142-24.122
137.945-3.37792.97535.6535-4.49136.01560.0277-1.5145-0.32391.29010.3935-1.06960.4852-0.1625-0.0151.64970.31080.02561.12170.15980.65441.4327-32.9019-14.5924
145.79791.235-0.51182.66320.02566.525-0.1160.09960.22950.2039-0.0778-0.0630.04960.65530.12110.28830.02370.00140.23830.03750.17791.8226-16.4129-18.187
158.5217-1.8217-0.82629.8047-0.55428.8796-0.02360.284-0.25380.7293-0.25931.84380.7982-1.15890.05250.9453-0.3456-0.12710.6231-0.05820.781-14.2725-30.0289-33.4752
165.76375.16155.9074.62625.29366.04810.7125-0.31672.13250.0039-0.61280.4586-0.9193-1.49430.39750.64430.19590.20530.61330.10910.7363-25.7666-5.6072-1.4032
173.94173.90293.44035.21982.21974.0086-0.26430.9362-1.386-0.45790.4646-0.48861.09180.4308-0.6161.5420.12210.1959-0.205-0.7040.0128-1.0464-37.6079-34.9368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305:322)A305 - 322
2X-RAY DIFFRACTION2chain 'A' and (resid 323:338)A323 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339:407)A339 - 407
4X-RAY DIFFRACTION4chain 'A' and (resid 408:455)A408 - 455
5X-RAY DIFFRACTION5chain 'A' and (resid 456:472)A456 - 472
6X-RAY DIFFRACTION6chain 'A' and (resid 473:528)A473 - 528
7X-RAY DIFFRACTION7chain 'A' and (resid 529:548)A529 - 548
8X-RAY DIFFRACTION8chain 'B' and (resid 306:338)B306 - 338
9X-RAY DIFFRACTION9chain 'B' and (resid 339:363)B339 - 363
10X-RAY DIFFRACTION10chain 'B' and (resid 364:407)B364 - 407
11X-RAY DIFFRACTION11chain 'B' and (resid 408:421)B408 - 421
12X-RAY DIFFRACTION12chain 'B' and (resid 422:455)B422 - 455
13X-RAY DIFFRACTION13chain 'B' and (resid 456:472)B456 - 472
14X-RAY DIFFRACTION14chain 'B' and (resid 473:530)B473 - 530
15X-RAY DIFFRACTION15chain 'B' and (resid 531:548)B531 - 548
16X-RAY DIFFRACTION16chain 'C' and (resid 687:696)C687 - 696
17X-RAY DIFFRACTION17chain 'D' and (resid 687:696)D687 - 696

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