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

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Basic information

Entry
Database: PDB / ID: 5tmv
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the OBHS analog, 4-iodophenyl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate
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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / 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 proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus 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 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / 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 / 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 / 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 / beta-catenin binding / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / 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-7FO / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsNwachukwu, J.C. / Erumbi, R. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Izard, T. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Nowak, J. / Wright, N.J. / Minutolo, F. / Rangarajan, E.S. / Izard, T. / Yao, X.Q. / Grant, B.J. / Kojetin, D.J. / Elemento, O. / Katzenellenbogen, J.A. / Nettles, K.W.
History
DepositionOct 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,8846
Polymers61,7594
Non-polymers1,1252
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-30 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.390, 81.520, 58.360
Angle α, β, γ (deg.)90.00, 110.61, 90.00
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 (UNP residues 298-554) / 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: 1579.866 Da / Num. of mol.: 2
Fragment: Nuclear receptor-interacting peptide (UNP residues 686-698)
Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-7FO / 4-iodophenyl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 562.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H19IO6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 1.96 Å3/Da / Density % sol: 37.27 % / Mosaicity: 1.447 °
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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.377→50 Å / Num. obs: 18809 / % possible obs: 97.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 28.97 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.2
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.874 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→46.23 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.36
RfactorNum. reflection% reflection
Rfree0.252 1568 9.95 %
Rwork0.193 --
obs0.199 15761 81.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.51 Å2
Refinement stepCycle: LAST / Resolution: 2.38→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 64 64 3988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024009
X-RAY DIFFRACTIONf_angle_d0.4875435
X-RAY DIFFRACTIONf_dihedral_angle_d11.8442406
X-RAY DIFFRACTIONf_chiral_restr0.033642
X-RAY DIFFRACTIONf_plane_restr0.002672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.377-2.45380.2156240.2198185X-RAY DIFFRACTION12
2.4538-2.54140.2921880.2239797X-RAY DIFFRACTION51
2.5414-2.64320.31841390.22931347X-RAY DIFFRACTION85
2.6432-2.76350.30581590.23061373X-RAY DIFFRACTION89
2.7635-2.90910.26621510.22221359X-RAY DIFFRACTION86
2.9091-3.09140.28181700.2151490X-RAY DIFFRACTION95
3.0914-3.330.26271650.21171529X-RAY DIFFRACTION97
3.33-3.6650.26421730.20481520X-RAY DIFFRACTION97
3.665-4.1950.24071590.1721458X-RAY DIFFRACTION92
4.195-5.28410.23111720.16071576X-RAY DIFFRACTION99
5.2841-46.24270.20351680.17391559X-RAY DIFFRACTION96
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)
10.01730.0020.00570.04610.02940.0272-0.01480.05080.175-0.0916-0.0237-0.0574-0.1028-0.07390.07070.34360.3897-0.16610.48490.18440.20351.653619.6422-4.5932
20.11980.0778-0.0550.0692-0.02720.03230.03820.2044-0.2365-0.183-0.0848-0.1120.06740.09140.00310.31130.1342-0.06720.3993-0.00320.344420.9422-4.9661-6.8545
30.19990.0547-0.25580.0878-0.02750.24820.08470.10810.19860.0529-0.0433-0.2961-0.19220.0897-0.00040.2221-0.00490.01520.16610.01240.241917.22918.08162.192
40.0517-0.0312-0.04290.03010.05280.0803-0.14190.1618-0.3410.1667-0.03930.09150.25540.0223-0.38650.538-0.16370.1482-0.1201-0.16930.314411.312-9.88273.2119
50.2350.0645-0.08970.3491-0.13420.14240.04380.27410.23350.14180.1312-0.1739-0.133-0.20640.20290.13420.0719-0.0220.2784-0.01430.18124.40749.19324.6122
60.7555-0.18610.07781.16290.1881.21820.2080.0720.16630.0874-0.40510.17430.2092-0.297-1.09840.17730.0511-0.01850.2358-0.03560.11022.93077.45648.5111
70.2374-0.0407-0.25660.02720.01850.30450.27480.09610.21890.1410.0071-0.23690.04950.22590.02280.1315-0.0054-0.03280.3217-0.01030.305428.00885.13859.0691
80.1381-0.0304-0.02720.543-0.16570.1047-0.0928-0.2565-0.12560.34850.18590.24770.1389-0.0790.08260.19360.0325-0.00020.5821-0.05980.2913-4.04245.589235.0612
90.2854-0.0968-0.28950.3838-0.00240.3592-0.3085-0.1803-0.1775-0.0140.00350.24080.35760.0707-0.19850.28410.0150.06550.2031-0.01720.24832.7394-0.742831.6186
10-0.00230.00120.00250.0032-0.00380.01440.30270.040.11590.05570.3183-0.1226-0.1343-0.06780.00020.37260.01350.00380.263-0.06120.33085.073217.569635.2695
110.09240.04790.03530.05160.06540.1022-0.0252-0.07050.01310.01220.0651-0.0664-0.16690.02540.07530.4776-0.17510.12280.7092-0.35960.543916.806915.861334.6047
120.0038-0.0006-0.01770.0038-0.00460.55570.05450.02920.0781-0.11190.1109-0.0321-0.45190.18820.06220.1946-0.01560.03730.1043-0.0190.23267.337717.046324.4452
130.0404-0.1022-0.02990.17840.0310.1992-0.13440.169-0.1036-0.12710.0607-0.00370.1094-0.3423-0.03070.2210.00140.0110.2736-0.07320.2054-3.13142.94321.5762
140.7588-0.353-0.07540.1897-0.04220.6316-0.07790.2010.1725-0.1315-0.0501-0.1620.2569-0.3348-0.18980.22960.03170.02590.342800.2088-2.38425.272417.4873
150.0282-0.02660.02530.0433-0.03150.0221-0.01860.0569-0.04230.08570.05210.01060.00130.05020.0170.19020.2637-0.13310.55370.22910.660714.7149-5.973732.5892
160.00820.0045-0.00130.00180.00040.00040.04590.00860.0994-0.0794-0.13360.0636-0.14680.0804-0.00010.2651-0.00330.04360.4566-0.050.648925.365818.46020.5175
170.0605-0.01580.01630.044-0.01260.1006-0.0843-0.0733-0.05940.00010.0353-0.0506-0.0244-0.1088-0.05420.66470.02540.05040.47820.23210.55470.1297-13.071635.7734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 304 THROUGH 321 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 322 THROUGH 338 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 339 THROUGH 394 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 395 THROUGH 437 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 438 THROUGH 470 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 471 THROUGH 531 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 532 THROUGH 548 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 304 THROUGH 338 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 339 THROUGH 394 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 395 THROUGH 407 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 408 THROUGH 421 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 422 THROUGH 438 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 439 THROUGH 465 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 466 THROUGH 528 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 529 THROUGH 548 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 688 THROUGH 697 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 688 THROUGH 697 )

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