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

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Basic information

Entry
Database: PDB / ID: 5dig
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in complex with a trifluoromethyl-substituted A-CD ring estrogen derivative (1S,3aR,5S,7aS)-5-[4-hydroxy-2-(trifluoromethyl)phenyl]-7a-methyloctahydro-1H-inden-1-ol
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 / prostate epithelial cord elongation / epithelial cell development / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone mediated signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nuclear signaling by ERBB4 / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / cellular response to hormone stimulus / protein localization to chromatin / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Regulation of lipid metabolism by PPARalpha / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / 14-3-3 protein binding / transcription corepressor binding / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / response to progesterone / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / nuclear receptor binding / circadian regulation of gene expression / euchromatin / 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 / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / male gonad development / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / 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-5CE / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 1, 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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / 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)62,5626
Polymers61,9334
Non-polymers6292
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-28 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.261, 84.179, 58.905
Angle α, β, γ (deg.)90.000, 108.930, 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-5CE / (1S,3aR,5S,7aS)-5-[4-hydroxy-2-(trifluoromethyl)phenyl]-7a-methyloctahydro-1H-inden-1-ol


Mass: 314.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21F3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
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: APS / Beamline: 23-ID-B / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 24833 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.564 / Net I/av σ(I): 28.294 / Net I/σ(I): 12.9 / Num. measured all: 90350
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.24-2.282.80.30211191.69888.7
2.28-2.323.20.27811861.11396.2
2.32-2.363.40.24712281.11698.6
2.36-2.413.50.25612471.14899.4
2.41-2.473.70.212591.1599.9
2.47-2.523.70.1912121.141100
2.52-2.593.80.16812671.147100
2.59-2.663.80.14612321.179100
2.66-2.733.70.13112471.227100
2.73-2.823.80.11512711.193100
2.82-2.923.80.09512391.329100
2.92-3.043.80.08412351.508100
3.04-3.183.80.07512561.712100
3.18-3.353.80.06512671.627100
3.35-3.563.80.04812311.561100
3.56-3.833.70.04612531.85999.7
3.83-4.223.70.04812692.299100
4.22-4.823.70.04712552.587100
4.82-6.083.70.04312692.028100
6.08-503.60.0412912.50199.5

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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: 2QA8

2qa8


Resolution: 2.24→42.09 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2122 1918 8.05 %
Rwork0.1859 21921 -
obs0.1881 23839 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.26 Å2 / Biso mean: 44.2879 Å2 / Biso min: 18.08 Å2
Refinement stepCycle: final / Resolution: 2.24→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 44 208 4202
Biso mean--31.61 43.23 -
Num. residues----503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024077
X-RAY DIFFRACTIONf_angle_d0.645523
X-RAY DIFFRACTIONf_chiral_restr0.023654
X-RAY DIFFRACTIONf_plane_restr0.005682
X-RAY DIFFRACTIONf_dihedral_angle_d12.5481503
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 (%)
2.2385-2.29450.3479980.29971173127171
2.2945-2.35650.23671350.23491446158189
2.3565-2.42580.24441320.21511496162892
2.4258-2.50410.25771280.20561561168994
2.5041-2.59360.23751330.21111572170596
2.5936-2.69740.24091520.20091578173096
2.6974-2.82020.27951460.20691600174698
2.8202-2.96880.25751410.20181602174398
2.9688-3.15480.22751400.19371623176399
3.1548-3.39830.20251380.19311619175799
3.3983-3.740.19791370.17641654179199
3.74-4.28080.19051470.155616471794100
4.2808-5.39160.18251420.155916661808100
5.3916-42.09690.18011490.181616841833100
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)
12.0691.2759-1.84413.8877-2.90152.6444-0.5779-0.12360.0647-0.56770.83610.9799-0.15430.4519-0.70560.8025-0.2482-0.16590.6366-0.11170.675419.864717.752529.367
22.56381.76220.98054.14564.47097.31310.0559-1.19430.65120.19410.1236-0.48950.57010.6199-0.20110.5395-0.0939-0.1230.5562-0.05580.386216.29256.302533.6402
35.36524.46840.63774.2165-0.19570.95030.0716-0.4953-0.15510.4335-0.28950.43530.53740.19250.07750.4946-0.0010.16420.4430.03090.5452-9.3454-8.82332.062
46.15622.8130.46285.35621.15922.74180.0702-0.25850.08990.408-0.02670.2757-0.1346-0.2256-0.13020.26040.04290.04730.25640.04070.2217-5.70771.264327.4342
52.34980.8574-0.45814.40580.37242.91940.2179-0.0920.4525-0.0877-0.0846-0.0176-0.65430.2323-0.13190.3508-0.01610.06380.2347-0.00130.3223.33718.268322.1628
63.94811.4956-2.09334.7036-0.143.5281-0.0762-0.3926-0.53170.2638-0.17730.10690.5852-0.17020.25350.38950.03640.06170.25160.00680.3246-3.2306-14.502924.0103
79.83773.21131.41692.50170.15232.2015-0.03450.3947-0.9142-0.1403-0.0389-0.17290.24450.28580.10230.34930.03820.01740.2693-0.02960.31014.8516-12.153817.856
85.8056-1.1037-0.84035.9479-1.59374.91690.1443-0.1486-0.19480.0116-0.1669-0.0450.17110.46810.05480.2215-0.01190.0080.3027-0.02540.247912.81780.576424.445
96.70483.6332-1.00754.11811.90257.00020.75950.20080.6398-2.7456-1.5150.0236-0.99610.5775-0.11750.9540.16350.18910.6689-0.00640.60988.230414.616912.5868
107.2724-2.4226-0.5573.8779-0.41034.3228-0.0938-0.25970.65630.7984-0.0444-0.2947-0.60680.36060.03290.2565-0.1208-0.00850.4516-0.04870.340820.96487.072122.5615
115.20010.7235-0.64080.945-0.6141.72720.0810.3437-0.2589-0.0486-0.01180.00810.07240.0444-0.06120.3070.0206-0.00810.2595-0.010.24136.4832-2.751914.2422
121.9171.12171.68611.05460.02833.58320.435-0.20620.70270.1363-0.32030.4284-0.5406-0.3655-0.15150.30060.08810.06280.32950.00780.5437-11.90795.416317.166
135.7998-0.20112.36061.76531.40082.53050.45240.6735-0.8231-0.3367-0.0404-0.64920.57151.3936-0.07840.37030.12230.04770.6131-0.02290.598829.9224-7.2512-1.2134
140.26940.06480.17160.334-0.1060.12080.02080.24860.275-0.5857-0.04140.0074-0.4310.16850.04180.77580.0378-0.02310.54920.07710.39717.83579.0093-17.8665
152.6967-0.72641.47883.1707-1.18255.11840.13270.1285-0.3239-0.3767-0.07210.01660.3231-0.0906-0.04880.3069-0.00430.01650.2708-0.01630.235610.4887-4.2208-6.3758
163.147-0.25440.28875.33960.09794.11020.00070.01740.3025-0.3823-0.0710.4289-0.7668-0.24030.17090.61690.0582-0.07140.31880.02390.3816.493614.8294-7.8269
176.1714-3.25655.77084.6873-2.68465.9323-0.1289-0.02081.53520.2713-0.211-0.0108-0.58750.03170.43270.41230.04090.04320.2624-0.02230.325910.582913.24792.3009
182.4101-0.08621.98876.48451.0394.0636-0.09910.18960.2267-0.23990.1077-0.1498-0.24150.37740.05570.26630.00290.05440.30220.0150.236520.62391.04911.8641
193.61793.5811-1.20273.9475-1.6010.8350.2699-0.66070.21920.8113-0.47230.06010.10310.50350.33920.560.11050.00510.8820.05420.4239.5141-14.74358.9365
203.45550.11230.16022.09190.13892.92290.07780.0134-0.26660.0717-0.0745-0.04110.17590.11730.01130.26760.00030.01930.25770.04480.276416.5417-0.98357.3284
217.85060.8655-5.06932.13690.63553.9918-0.01170.69620.1152-0.86070.00120.8722-0.0531-0.8770.0850.55190.001-0.07470.4764-0.03250.4574-3.1842-5.2173-8.0816
220.31720.103-0.12720.0546-0.0450.04420.5769-0.52950.499-0.1799-0.0059-0.2481-0.5098-0.21480.00120.51420.0180.17060.4242-0.01490.5862-6.540517.26826.8024
230.02940.1024-0.08141.1816-1.07641.0597-0.028-0.0975-0.4134-0.505-0.51620.01530.93020.1167-0.1220.79970.0025-0.0460.5819-0.04090.53138.2454-16.3004-11.2202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 303 through 311 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 312 through 322 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 323 through 338 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 339 through 363 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 364 through 394 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 395 through 420 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 421 through 438 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 439 through 455 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 456 through 470 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 471 through 496 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 497 through 531 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 532 through 550 )A0
13X-RAY DIFFRACTION13chain 'B' and (resid 305 through 322 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 323 through 338 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 339 through 394 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 395 through 421 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 422 through 438 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 439 through 455 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 456 through 466 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 467 through 530 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 531 through 549 )B0
22X-RAY DIFFRACTION22chain 'C' and (resid 687 through 696 )C0
23X-RAY DIFFRACTION23chain 'D' and (resid 687 through 696 )D0

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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