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

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Basic information

Entry
Database: PDB / ID: 5tmq
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the Arene Core OBHS derivative, 4-bromophenyl 4,4''-dihydroxy-[1,1':2',1''-terphenyl]-4'-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 / 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 / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / 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 / 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-7M7 / 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. / 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)62,7546
Polymers61,7594
Non-polymers9952
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-29 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 82.010, 58.090
Angle α, β, γ (deg.)90.000, 110.980, 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, UNP residues 125-381 / 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-7M7 / 4-bromophenyl 4,4''-dihydroxy-[1,1':2',1''-terphenyl]-4'-sulfonate


Mass: 497.358 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H17BrO5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.97 Å3/Da / Density % sol: 37.48 % / Mosaicity: 1.652 °
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: 2.24→46.352 Å / Num. obs: 22865 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 31.68 Å2 / Rmerge(I) obs: 0.096 / Χ2: 0.889 / Net I/av σ(I): 21.389 / Net I/σ(I): 5 / Num. measured all: 154652
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.24-2.286.50.746199.7
2.28-2.326.70.648199.7
2.32-2.366.80.607199.7
2.36-2.416.80.522198.9
2.41-2.476.80.445199
2.47-2.526.80.402199.3
2.52-2.596.80.328198.9
2.59-2.666.80.288198.5
2.66-2.736.50.236196.8
2.73-2.825.90.215196.6
2.82-2.926.90.176199.6
2.92-3.047.10.147199.9
3.04-3.187.10.131199.9
3.18-3.3570.115199.9
3.35-3.566.90.095198.7
3.56-3.836.80.087198.3
3.83-4.226.10.081196.8
4.22-4.827.20.078199.7
4.82-6.0870.075199.2
6.08-506.60.059197.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→46.352 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.17
RfactorNum. reflection% reflection
Rfree0.2419 1863 8.71 %
Rwork0.1957 --
obs0.1998 21396 92.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.45 Å2 / Biso mean: 49.8624 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 2.24→46.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3869 0 62 114 4045
Biso mean--55.62 37.93 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024041
X-RAY DIFFRACTIONf_angle_d0.4595481
X-RAY DIFFRACTIONf_chiral_restr0.032643
X-RAY DIFFRACTIONf_plane_restr0.003679
X-RAY DIFFRACTIONf_dihedral_angle_d14.2212417
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 (%)
2.2386-2.29910.3023950.2313961105660
2.2991-2.36670.29381330.24271438157189
2.3667-2.44310.30821410.23581450159190
2.4431-2.53040.25051440.23091505164992
2.5304-2.63170.30351290.22971507163693
2.6317-2.75150.29091500.22061518166893
2.7515-2.89660.28321470.2231542168995
2.8966-3.0780.24911590.22281573173298
3.078-3.31560.26911430.2161606174999
3.3156-3.64910.23561600.19151593175398
3.6491-4.17690.19741500.16851583173397
4.1769-5.26120.21021530.157916321785100
5.2612-46.36220.21921590.17981625178498
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)
1-0.0028-0.00960.0020.07720.0131-0.00010.1320.03880.0173-0.03220.03790.102-0.0584-0.13560.22540.2380.8373-0.24050.50520.32580.11040.669518.2636-5.3562
20.14260.0702-0.02580.0404-0.00840.0236-0.03060.2222-0.1383-0.0993-0.1064-0.10010.11450.2441-0.01920.25180.1718-0.05570.39270.00950.210620.9571-6.4282-6.5412
30.28670.0102-0.27420.11040.08560.25090.17210.0420.05110.1082-0.0536-0.1049-0.05960.01280.00330.20660.02820.02990.15850.02050.233416.85867.99442.296
40.0062-0.01130.00890.0413-0.07310.1776-0.06670.0974-0.0881-0.0766-0.1633-0.17630.45760.0046-0.01850.397-0.07790.08060.2343-0.0960.370811.7528-9.5443-2.9569
50.0114-0.01150.0010.01180.00270.0046-0.1589-0.05570.04420.01850.0224-0.11940.0954-0.0062-01.26590.07530.24790.342-0.01380.887319.1161-14.88788.1565
60.4949-0.1817-0.73310.19530.46211.1895-0.03870.3386-0.26330.1228-0.24930.11640.3724-0.6925-0.16750.18310.0601-0.00830.2190.00030.22624.26210.01574.0382
70.0023-0.00160.00510.0046-0.00270.00440.0985-0.05690.07320.05390.08470.0951-0.0140.045500.647-0.01890.19660.238-0.06010.603610.327817.320115.0119
80.5766-0.1035-0.11240.42360.2620.64490.35730.43320.1236-0.037-0.5004-0.1090.1609-0.1461-0.45310.15820.118-0.04150.31890.01190.21672.596.50248.3319
90.01280.00770.01680.00390.01140.01480.1256-0.0403-0.0202-0.1128-0.0658-0.13680.11290.327100.36490.0401-0.04210.4293-0.00480.511327.99054.73748.7059
100.0460.0067-0.05620.2881-0.19940.1562-0.20870.0161-0.21580.22220.11670.13210.1376-0.0116-0.00390.2626-0.00150.03530.5093-0.08790.301-4.20745.489434.699
110.6387-0.0573-0.61470.30760.04690.9669-0.2898-0.3681-0.107-0.01620.0262-0.00030.50580.3048-0.45020.2911-0.04460.01930.0265-0.02220.17822.86762.31832.0134
120.1212-0.0772-0.20490.06020.19820.4868-0.0371-0.1820.0218-0.27630.0759-0.1557-0.489-0.02550.02830.3308-0.07660.0140.3042-0.07050.29375.121113.262526.7949
130.2713-0.09990.14810.036-0.05130.0808-0.0722-0.04010.1554-0.0853-0.001-0.05350.02260.0343-0.10380.7128-0.1570.27530.446-0.16190.4120.8596-10.488714.936
140.441-0.139-0.26120.5727-0.16370.8871-0.1015-0.34910.1649-0.0886-0.0785-0.1567-0.0045-0.3984-0.26940.19290.0498-0.03690.3462-0.00090.2089-1.40235.342518.2933
150.01-0.0138-0.00440.0121-00.0011-0.02990.0319-0.0132-0.05780.03010.00510.0113-0.01170.02060.44380.20690.04350.34070.23350.482315-5.584233.3205
160.00130.00330.00150.00980.00760.0032-0.0241-0.079-0.0785-0.0772-0.14820.003-0.04890.054-0.00010.4699-0.0710.25820.3674-0.07990.79425.296217.87981.1522
170.0071-0.022-0.02320.07330.08060.0858-0.0347-0.0439-0.09030.0341-0.04710.02810.0851-0.0471-0.04940.7975-0.01680.09830.12850.06810.66630.5502-13.30535.7379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 321 )A305 - 321
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A322 - 338
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 394 )A339 - 394
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 411 )A395 - 411
5X-RAY DIFFRACTION5chain 'A' and (resid 412 through 421 )A412 - 421
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 455 )A422 - 455
7X-RAY DIFFRACTION7chain 'A' and (resid 456 through 472 )A456 - 472
8X-RAY DIFFRACTION8chain 'A' and (resid 473 through 531 )A473 - 531
9X-RAY DIFFRACTION9chain 'A' and (resid 532 through 548 )A532 - 548
10X-RAY DIFFRACTION10chain 'B' and (resid 303 through 338 )B303 - 338
11X-RAY DIFFRACTION11chain 'B' and (resid 339 through 407 )B339 - 407
12X-RAY DIFFRACTION12chain 'B' and (resid 408 through 455 )B408 - 455
13X-RAY DIFFRACTION13chain 'B' and (resid 456 through 467 )B456 - 467
14X-RAY DIFFRACTION14chain 'B' and (resid 468 through 531 )B468 - 531
15X-RAY DIFFRACTION15chain 'B' and (resid 532 through 548 )B532 - 548
16X-RAY DIFFRACTION16chain 'C' and (resid 688 through 696 )C688 - 696
17X-RAY DIFFRACTION17chain 'D' and (resid 688 through 697 )D688 - 697

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