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- PDB-4znt: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 4znt
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in complex with a 3-Bromo-substituted OBHS derivative
Components
  • Estrogen receptor
  • Nuclear receptor-interacting peptide
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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / steroid binding / : / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / 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 / Transcriptional activation of mitochondrial biogenesis / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / 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-OBB / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 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
DepositionMay 5, 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-interacting peptide
D: Nuclear receptor-interacting peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8496
Polymers61,8194
Non-polymers1,0312
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-27 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.340, 81.810, 58.740
Angle α, β, γ (deg.)90.000, 111.020, 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: 29329.457 Da / Num. of mol.: 2 / Fragment: ligand-binding domain, UNP residues 301-559 / 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-interacting peptide / 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: UNP residues 686-698 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-OBB / 3-bromophenyl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 515.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H19BrO6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.14 Å3/Da / Density % sol: 42.58 %
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: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 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: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 37775 / % possible obs: 97.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.099 / Net I/av σ(I): 37.372 / Net I/σ(I): 8.4 / Num. measured all: 253074
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.936.50.7118760.52998.9
1.93-1.976.70.62419060.49798.5
1.97-2.016.70.49518760.51798.9
2.01-2.056.70.41419320.56898.8
2.05-2.096.60.33518900.61398.8
2.09-2.146.40.27118750.63598.8
2.14-2.196.10.20318490.71695.5
2.19-2.256.90.19119040.79898.7
2.25-2.3270.16518790.75998.6
2.32-2.3970.1419160.82498.9
2.39-2.486.90.12218990.88998.8
2.48-2.586.90.10619010.99599.3
2.58-2.76.80.09219431.11499.3
2.7-2.846.30.08118351.29795.2
2.84-3.027.10.07518921.48599
3.02-3.2570.06919481.68798.9
3.25-3.586.80.06518801.9897.8
3.58-4.096.10.06117932.27392.4
4.09-5.166.70.05618492.23594.9
5.16-506.70.04219321.65396.6

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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: 1.903→46.928 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 1714 5.26 %
Rwork0.1956 30877 -
obs0.1966 32591 84.9 %
Solvent computationShrinkage radii: 1.25 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.403 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 165.9 Å2 / Biso mean: 38.8668 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.2203 Å2-0 Å20.1242 Å2
2---0.9893 Å20 Å2
3---0.7691 Å2
Refinement stepCycle: final / Resolution: 1.903→46.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3753 0 64 235 4052
Biso mean--37.68 40.31 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033976
X-RAY DIFFRACTIONf_angle_d0.6635399
X-RAY DIFFRACTIONf_chiral_restr0.047635
X-RAY DIFFRACTIONf_plane_restr0.002671
X-RAY DIFFRACTIONf_dihedral_angle_d14.2051471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.903-1.95850.2461360.205858920
1.9585-2.02170.2629950.2316182961
2.0217-2.0940.27651440.2407256385
2.094-2.17780.23361450.2244264188
2.1778-2.2770.2611530.2117275191
2.277-2.3970.24991620.1995290495
2.397-2.54720.23811590.1945293297
2.5472-2.74380.22631670.2036295198
2.7438-3.01990.231600.2026289296
3.0199-3.45680.22111710.1992299698
3.4568-4.35470.19191600.1741283393
4.3547162299696
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)
12.00391.43120.25331.58580.01590.29230.055-0.29910.40130.3711-0.0834-0.0207-0.40010.44570.1980.4839-0.3621-0.01790.5043-0.1730.1893-6.1198-10.19376.0284
25.3505-1.3528-2.2882.2256-0.94343.35840.2754-0.89760.62230.47940.26860.5668-0.4082-0.3142-0.7710.5568-0.20360.22760.4003-0.09060.6262-25.999-36.17011.9869
32.7839-0.0413-0.44571.4696-0.38022.9280.0411-0.04650.19970.1647-0.09270.1493-0.1198-0.26560.08850.1662-0.0490.02870.1017-0.03520.1399-16.4196-16.042-1.8609
40.7628-0.4888-0.9581.2455-0.63562.8235-0.47470.0769-0.6775-0.2099-0.07060.24291.1072-0.2187-0.3550.5403-0.05280.19820.1881-0.00790.3983-13.3583-34.118-4.175
55.6021-1.48910.89215.4788-2.165.18580.1644-0.1553-0.13280.1381-0.3549-0.12840.08690.60410.33240.1774-0.0803-0.01360.216-0.0070.1346-2.9956-17.6769-3.6585
62.6499-0.4858-0.54282.77990.11853.25010.2218-0.40610.46050.2315-0.3049-0.294-0.36570.54450.09640.3204-0.1522-0.06510.3388-0.00250.21995.0483-10.7808-5.4
75.25410.8617-0.88662.6114-0.23732.8877-0.19330.2108-0.18790.0301-0.06160.27630.3322-0.30540.14210.2006-0.06980.01330.1058-0.02770.1058-10.6677-22.6467-13.235
80.2182-0.8767-0.4575.15263.84583.43420.4675-0.4694-0.23320.8891-0.1513-0.11841.148-0.2593-0.73751.3536-0.4485-0.03351.0653-0.38460.6904-31.4497-27.1104-10.4894
95.46020.5643-2.43696.0772-3.26612.9197-0.34240.86170.2255-0.4320.28540.8710.6444-1.1983-0.04660.3703-0.14610.03230.5275-0.06930.4388-26.97-16.2182-9.0811
105.66-0.91292.12973.0927-0.2184.014-0.1993-0.4169-0.37490.02480.1567-0.64380.27380.52250.07920.14240.00170.05480.47890.03820.317111.7599-20.196-30.5875
111.85490.89841.84840.73330.90142.69220.0465-0.0963-0.02840.02130.07390.15650.0988-0.2015-0.18220.34180.0275-0.18171.32650.1180.5433-15.0821-10.726-49.1883
121.6068-0.0289-0.67632.2535-0.39540.7423-0.29310.38490.9026-0.2014-0.02120.2254-0.2364-0.17570.41350.2212-0.0074-0.13091.13330.15950.4983-19.5607-15.1247-41.0314
131.99331.1866-0.64572.51210.35623.3195-0.28090.277-0.2386-0.10620.1273-0.02290.3394-0.1608-0.00150.1039-0.01290.00950.1486-0.00530.0966-2.8048-20.4656-32.2862
144.1096-0.49760.96513.34990.07693.923-0.11130.06050.20540.18230.11250.2346-0.4167-0.19720.08550.15790.01170.02880.17220.04980.0998-4.2892-12.9282-25.0784
154.13612.57691.39811.84021.00112.48940.63130.0651-1.45630.4878-0.74052.00320.5857-0.05220.09811.82790.24160.0630.7054-0.03621.02223.4852-39.0565-15.012
163.15570.77940.22571.66461.24262.2503-0.0455-0.1816-0.00920.3679-0.1658-0.52360.05691.0519-0.74890.0173-0.1382-0.14790.37090.04110.16119.5434-15.233-15.2225
175.55351.62892.10553.89470.57923.7676-0.33550.1558-0.0765-0.0232-0.03930.41240.1882-0.62220.17970.1201-0.0240.04120.2271-0.03390.1702-12.1191-18.6089-22.2349
182.2921.06162.10654.1377-1.28125.34070.2783-0.1283-0.46080.2237-0.03330.55490.4895-0.90480.00170.4915-0.35120.00390.5661-0.11450.4221-13.6686-30.2158-31.8023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 305:329)A305 - 329
2X-RAY DIFFRACTION2(chain A and resid 330:339)A330 - 339
3X-RAY DIFFRACTION3(chain A and resid 340:397)A340 - 397
4X-RAY DIFFRACTION4(chain A and resid 398:434)A398 - 434
5X-RAY DIFFRACTION5(chain A and resid 435:459)A435 - 459
6X-RAY DIFFRACTION6(chain A and resid 460:504)A460 - 504
7X-RAY DIFFRACTION7(chain A and resid 505:527)A505 - 527
8X-RAY DIFFRACTION8(chain A and resid 528:535)A528 - 535
9X-RAY DIFFRACTION9(chain A and resid 536:548)A536 - 548
10X-RAY DIFFRACTION10(chain B and resid 305:329)B305 - 329
11X-RAY DIFFRACTION11(chain B and resid 330:336)B330 - 336
12X-RAY DIFFRACTION12(chain B and resid 337:343)B337 - 343
13X-RAY DIFFRACTION13(chain B and resid 344:413)B344 - 413
14X-RAY DIFFRACTION14(chain B and resid 414:460)B414 - 460
15X-RAY DIFFRACTION15(chain B and resid 461:471)B461 - 471
16X-RAY DIFFRACTION16(chain B and resid 472:511)B472 - 511
17X-RAY DIFFRACTION17(chain B and resid 512:525)B512 - 525
18X-RAY DIFFRACTION18(chain B and resid 526:548)B526 - 548

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