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Basic information

Entry
Database: PDB / ID: 5did
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in complex with a difluoro-substituted A-CD ring estrogen derivative (1S,3aR,5S,7aS)-5-(2,3-difluoro-4-hydroxyphenyl)-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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / regulation of branching involved in prostate gland morphogenesis / 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 / 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 / regulation of lipid metabolic process / androgen 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 / estrogen receptor signaling pathway / 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 / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / 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 / stem cell differentiation / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / 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 / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / ATPase binding / 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-5CK / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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
DepositionAug 31, 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)62,4986
Polymers61,9334
Non-polymers5652
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-33 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.942, 82.990, 58.273
Angle α, β, γ (deg.)90.000, 109.020, 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 / 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-5CK / (1S,3aR,5S,7aS)-5-(2,3-difluoro-4-hydroxyphenyl)-7a-methyloctahydro-1H-inden-1-ol


Mass: 282.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20F2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 43.52 %
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: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 22338 / % possible obs: 91.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Χ2: 1.152 / Net I/av σ(I): 18.429 / Net I/σ(I): 10.1 / Num. measured all: 75300
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.24-2.282.20.2555551.07645.7
2.28-2.322.30.2737261.09759.2
2.32-2.362.40.2788181.02668.3
2.36-2.412.60.2789541.09578.7
2.41-2.472.60.26910731.03988.7
2.47-2.522.80.28211441.08193.9
2.52-2.5930.26711721.14496.5
2.59-2.663.20.23912201.10298.1
2.66-2.733.50.23511751.0699
2.73-2.823.60.21412001.09599.6
2.82-2.923.70.16912391.13100
2.92-3.043.80.14412271.232100
3.04-3.183.80.12312141.318100
3.18-3.353.80.09812111.279100
3.35-3.563.80.06312201.082100
3.56-3.833.80.04912161.092100
3.83-4.223.80.04812471.408100
4.22-4.823.80.04212251.468100
4.82-6.083.80.03412350.991100
6.08-503.70.02312670.89899.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.24→46.459 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 1905 9.04 %
Rwork0.1843 19163 -
obs0.1882 21068 86.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.51 Å2 / Biso mean: 41.7543 Å2 / Biso min: 16.86 Å2
Refinement stepCycle: final / Resolution: 2.24→46.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 40 173 4199
Biso mean--30.19 37.5 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034101
X-RAY DIFFRACTIONf_angle_d0.6395555
X-RAY DIFFRACTIONf_chiral_restr0.023662
X-RAY DIFFRACTIONf_plane_restr0.003687
X-RAY DIFFRACTIONf_dihedral_angle_d13.9831497
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 (%)
2.2388-2.29480.3096650.236567674143
2.2948-2.35680.3488790.24591699557
2.3568-2.42620.26921120.2351089120170
2.4262-2.50450.30221330.23731241137480
2.5045-2.5940.3051320.22651375150787
2.594-2.69780.23981450.22281424156991
2.6978-2.82060.27651430.22031488163194
2.8206-2.96930.23851490.20171527167695
2.9693-3.15530.26241540.20311514166897
3.1553-3.39880.20851510.1931571172298
3.3988-3.74070.21771580.16961568172699
3.7407-4.28170.20961570.14971575173299
4.2817-5.39320.18361610.156415831744100
5.3932-46.46950.21061660.16851616178299
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)
15.57961.90091.74913.40611.91412.06160.2686-0.94480.36330.4056-0.21160.24580.0617-0.0755-0.01170.33620.02680.01180.41970.03120.23724.01820.1931.8772
22.79040.3978-0.59223.0943-0.5382.14310.0401-0.144-0.03360.28770.02860.1372-0.0393-0.0113-0.06820.19290.02210.02460.21780.00640.15670.0105-3.226323.0205
34.331-1.5873-0.19014.6059-0.23482.41470.14310.07460.42450.0088-0.1371-0.3664-0.3880.2375-0.00090.2228-0.03530.01130.3066-0.04070.230116.03197.378320.8828
43.72510.9142-0.53881.1786-0.20890.8804-0.06040.36750.264-0.0120.02260.17140.0196-0.1083-0.05740.25410.0202-0.01220.2458-0.00110.20960.7897-0.2715.037
54.949-2.04082.95474.8505-1.15855.28450.17940.963-0.1443-0.8443-0.1741-0.15940.08140.7173-0.0970.423-0.11080.13480.4437-0.00350.290218.84350.6284-9.3325
62.91460.38590.71382.82360.14743.0213-0.13780.21050.0841-0.42770.09370.1056-0.21560.00770.1020.3514-0.00590.0260.2739-0.00160.18719.31523.5573-5.2637
72.92550.98670.94964.17190.37543.4877-0.0278-0.2049-0.5503-0.0374-0.0601-0.24710.40220.09030.13890.21120.04730.03840.26380.02070.267421.2235-5.5896.6153
83.48580.75292.10722.00430.6634.37190.1013-0.08050.0899-0.1985-0.16680.2940.1108-0.55780.04480.27370.03840.02740.27050.03080.29615.76590.50451.6582
95.25350.2853-2.42466.13480.1821.18120.2203-0.36860.7901-0.0608-0.40560.0529-1.0966-0.36490.03470.56950.01510.15870.402-0.13470.5485-6.330216.863926.7219
104.571-0.43843.10796.62170.00244.68110.16190.6056-0.8569-0.4836-0.22430.39691.6293-0.21930.10.81270.0021-0.0620.4204-0.05730.63758.1611-16.4657-11.207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 338 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 438 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 439 through 496 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 497 through 550 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 305 through 338 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 339 through 437 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 438 through 496 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 497 through 549 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 687 through 696 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 687 through 696 )D0

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