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Basic information

Entry
Database: PDB / ID: 5dwj
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with a Resorcinyl 4-Fluoro-substituted Diaryl-imine analog 4-[(E)-[(4-fluorophenyl)imino](4-hydroxyphenyl)methyl]benzene-1,3-diol
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 / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / 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-5J2 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsNwachukwu, J.C. / Wright, N.J. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. ...Nwachukwu, J.C. / Wright, N.J. / 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 22, 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)62,5806
Polymers61,9334
Non-polymers6472
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-29 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.996, 82.229, 58.420
Angle α, β, γ (deg.)90.000, 110.370, 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-5J2 / 4-[(E)-[(4-fluorophenyl)imino](4-hydroxyphenyl)methyl]benzene-1,3-diol


Mass: 323.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14FNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.01 Å3/Da / Density % sol: 38.66 %
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: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: channel-cut Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32176 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Χ2: 1.08 / Net I/av σ(I): 26.013 / Net I/σ(I): 10.4 / Num. measured all: 116715
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.033.40.92415870.85895.9
2.03-2.073.50.79315730.83596.3
2.07-2.113.50.76516050.91696.5
2.11-2.153.40.49315301.74294
2.15-2.23.60.53315611.02295.4
2.2-2.253.60.33315890.9296.8
2.25-2.313.60.31815880.94796.1
2.31-2.373.60.26115850.93497.5
2.37-2.443.60.20315990.95497.3
2.44-2.523.60.17416210.96897.6
2.52-2.613.70.1516281.04698.5
2.61-2.713.70.11916081.01998.6
2.71-2.843.70.09916381.07798.5
2.84-2.993.70.07916151.23998.9
2.99-3.173.70.06416501.34199
3.17-3.423.70.04816531.26999.4
3.42-3.763.70.03816281.27699.3
3.76-4.313.60.0316591.15499.4
4.31-5.433.80.02516591.05599.6
5.43-503.70.02116001.01693.8

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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: 2.001→32.88 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1784 6.12 %
Rwork0.2021 27353 -
obs0.204 29137 88.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.64 Å2 / Biso mean: 57.9095 Å2 / Biso min: 24.44 Å2
Refinement stepCycle: final / Resolution: 2.001→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3722 0 48 133 3903
Biso mean--42.02 52.94 -
Num. residues----479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023838
X-RAY DIFFRACTIONf_angle_d0.5725197
X-RAY DIFFRACTIONf_chiral_restr0.02619
X-RAY DIFFRACTIONf_plane_restr0.002644
X-RAY DIFFRACTIONf_dihedral_angle_d12.2681379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0006-2.05470.32291100.33471729183972
2.0547-2.11510.35431110.30611737184873
2.1151-2.18340.31991000.2991652175270
2.1834-2.26140.29621400.27132016215685
2.2614-2.35190.31911200.25162017213784
2.3519-2.45890.2711370.23222082221988
2.4589-2.58850.24591440.22562223236793
2.5885-2.75060.25051580.22472244240295
2.7506-2.96290.22621560.22262262241896
2.9629-3.26080.25761480.21992333248197
3.2608-3.73210.22241530.1892352250599
3.7321-4.69980.19371550.15982362251799
4.6998-32.88460.20621520.17772344249696
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)
14.67320.058-1.59322.4544-1.29795.93430.041-0.30220.04520.2857-0.07790.15620.1934-0.04090.0590.3418-0.04810.03090.2867-0.04110.2172-14.3852-19.60811.0981
25.18430.5395-1.30986.20580.23055.4576-0.18110.1007-0.3801-0.0659-0.10170.06060.94810.08560.18710.4307-0.02210.08480.2802-0.02690.204-8.1736-25.0716-6.4823
37.82870.3895-0.22882.6858-0.40995.63670.0814-0.09-0.0729-0.0093-0.10580.04020.1855-0.01380.03730.4043-0.01840.01530.24710.00970.1563-8.2538-18.2105-8.3277
44.0611.62-1.81044.1680.16667.2085-0.34480.4427-0.3145-0.10030.2098-0.18090.58050.3090.16290.33550.00980.08590.30350.020.2981.0535-22.4238-34.8031
53.67520.3113-2.85074.9752-0.31258.20510.04440.4910.28810.11360.10260.3759-0.4124-0.8292-0.18830.29510.0335-0.00810.34860.040.2384-6.5582-14.4207-29.495
64.50721.47320.26134.22041.21548.2841-0.0037-0.3466-0.15770.3536-0.129-0.32540.47241.45350.08080.27690.08050.03050.60580.05580.32767.8647-19.7347-19.2383
74.96011.2727-0.12073.92710.74028.3758-0.15430.2895-0.2709-0.267-0.02680.37390.4085-0.98920.08440.4029-0.0090.07150.33880.02570.3139-8.9468-21.3461-24.1405
80.0694-0.0474-0.0150.11130.05420.00960.66680.24660.8419-0.083-1.06170.6936-1.0186-1.1812-0.00030.64160.11450.15740.77410.00520.8326-26.2493-6.5968-1.8682
90.051-0.02940.05210.06660.03120.0589-0.11940.6139-1.38720.0250.0007-0.25980.33540.5328-0.00041.3196-0.0290.16210.549-0.0630.6518-1.1522-38.1806-35.6407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 411 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 412 through 472 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 473 through 548 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 305 through 371 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 372 through 437 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 438 through 496 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 497 through 549 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 687 through 696 )C0
9X-RAY DIFFRACTION9chain 'D' and (resid 688 through 696 )D0

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