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- PDB-5egv: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Entry
Database: PDB / ID: 5egv
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex the 3,4-diaryl-furan derivative 3-chloranyl-4-[4-(2-chloranyl-4-oxidanyl-phenyl)furan-3-yl]phenol
Components
  • Estrogen receptor
  • NCOA2
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / 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 / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Mitochondrial unfolded protein response (UPRmt) / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / : / steroid binding / positive regulation of adipose tissue development / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to estrogen / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / 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) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / Nuclear receptor coactivators bHLH domain / 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 / Double treble clef zinc finger, C4 type / 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-5OS / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.863 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
DepositionOct 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: NCOA2
D: NCOA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5756
Polymers61,9334
Non-polymers6422
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-29 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.510, 81.990, 58.620
Angle α, β, γ (deg.)90.000, 110.600, 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 NCOA2


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-5OS / 3-chloranyl-4-[4-(2-chloranyl-4-oxidanyl-phenyl)furan-3-yl]phenol


Mass: 321.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10Cl2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
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 31, 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: 2.86→50 Å / Num. obs: 11331 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.17 / Χ2: 1.296 / Net I/av σ(I): 15.489 / Net I/σ(I): 4.4 / Num. measured all: 72627
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.86-2.916.60.7485810.5499.8
2.91-2.966.50.6875630.563100
2.96-3.026.60.6025490.63299.8
3.02-3.086.50.5985940.64699.5
3.08-3.156.60.4675580.66299.8
3.15-3.226.60.4455570.68199.8
3.22-3.36.50.4145690.78599.1
3.3-3.396.50.3175580.92498.9
3.39-3.496.40.2985750.98399
3.49-3.66.60.295631.14498.9
3.6-3.736.20.2895631.96898.6
3.73-3.886.10.2075601.49198.2
3.88-4.065.50.1875401.63494.4
4.06-4.275.90.1835531.75296.7
4.27-4.546.80.1525761.58399.8
4.54-4.896.70.1355701.541100
4.89-5.386.70.1315721.50899.5
5.38-6.166.50.1385751.34198.5
6.16-7.7560.1135631.80197.6
7.75-506.10.0935924.0798.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 2.863→46.845 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 1001 10.06 %
Rwork0.2191 8945 -
obs0.225 9946 86.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.42 Å2 / Biso mean: 51.9321 Å2 / Biso min: 14.85 Å2
Refinement stepCycle: final / Resolution: 2.863→46.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 42 5 3697
Biso mean--50.76 20.36 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023763
X-RAY DIFFRACTIONf_angle_d0.5275106
X-RAY DIFFRACTIONf_chiral_restr0.019616
X-RAY DIFFRACTIONf_plane_restr0.002636
X-RAY DIFFRACTIONf_dihedral_angle_d11.5971342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8633-3.01430.307740.252771178549
3.0143-3.20310.34411560.26951279143587
3.2031-3.45030.33081490.25621361151093
3.4503-3.79740.33391420.23371304144690
3.7974-4.34660.24741560.19751387154394
4.3466-5.47490.2481590.19391452161198
5.4749-46.85080.22111650.20061451161697
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)
13.89141.1429-1.3514.1365-2.81272.2974-0.2166-0.258-0.0422-0.3180.1610.0111-0.5509-0.01140.11840.525-0.10770.10630.3663-0.08770.1834-14.7894-17.47623.3903
22.391-1.4-0.79212.6471-1.71553.7336-0.3485-0.049-0.20620.10970.15060.13870.26070.04730.09550.5138-0.03890.01350.3181-0.03790.1796-12.2094-24.1755-3.6658
34.48240.9073-0.56551.8803-0.56252.41070.38680.060.4110.2734-0.25230.06160.22510.1233-0.11360.4593-0.07540.02560.2615-0.0440.0837-7.3184-16.508-7.6542
43.19310.08130.57874.8008-0.97655.9617-0.19590.63980.1744-0.14390.0533-0.4255-0.01140.15210.21730.2682-0.03320.05040.33230.00070.18062.1113-17.4562-36.3662
52.584-0.04170.24885.1119-1.75445.6248-0.06440.2826-0.0574-0.15790.08950.05210.2115-0.21830.02790.2865-0.01930.01540.325-0.06340.1541-4.4688-19.9806-32.794
63.6309-0.3430.66622.8772-0.11275.5698-0.03360.17030.1890.879-0.2436-0.033-0.02660.47970.07710.35060.02880.05770.38810.02890.16652.8614-16.8809-20.9891
72.580.65740.93633.19090.72985.3485-0.0723-0.2717-0.57620.05850.05670.23820.2151-0.49250.11650.2652-0.0885-0.00160.38360.03310.2607-8.6285-20.8668-24.1411
80.10390.1107-0.0520.3686-0.30910.27890.1606-0.01710.33820.3101-0.45920.1829-0.2408-0.2537-0.01840.52720.07460.24050.4827-0.03720.5683-25.9625-6.6566-1.4374
90.2747-0.1449-0.08990.1775-0.07730.1751-0.1952-0.0063-0.19640.10330.42850.00230.03650.19870.38720.52460.06320.37760.425-0.14540.2549-0.771-37.5281-35.8735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 362 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 363 through 438 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 439 through 548 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 308 through 341 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 342 through 420 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 421 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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