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

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Basic information

Entry
Database: PDB / ID: 4znu
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in complex with a 2-Methyl-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 / 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-4Q9 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
C: Nuclear receptor-interacting peptide
B: Estrogen receptor
D: Nuclear receptor-interacting peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7206
Polymers61,8194
Non-polymers9012
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-26 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.960, 82.270, 58.500
Angle α, β, γ (deg.)90.000, 111.050, 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-4Q9 / 2-methylphenyl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 450.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
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: Jan 17, 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: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19202 / % possible obs: 98.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.082 / Χ2: 0.991 / Net I/av σ(I): 25.861 / Net I/σ(I): 6.1 / Num. measured all: 129718
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.4460.7879350.4696.1
2.44-2.495.80.7949220.4796.1
2.49-2.536.30.7059320.48197.3
2.53-2.5970.6429580.49699.3
2.59-2.6470.5099800.50199.5
2.64-2.770.4239600.55799.5
2.7-2.7770.3759530.58299.7
2.77-2.8570.3339700.59399.5
2.85-2.9370.2429850.6899.7
2.93-3.026.90.1999250.77698.6
3.02-3.136.70.1719780.91298.4
3.13-3.266.10.1529510.99996.5
3.26-3.4170.1299511.17999.1
3.41-3.587.20.1139731.38299.5
3.58-3.817.10.0979691.5899.5
3.81-4.16.90.0869731.83899.8
4.1-4.526.80.0779631.82498.7
4.52-5.176.50.0669431.67796.2
5.17-6.517.10.0639971.28899.7
6.51-506.70.0439841.3297.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXmodel building
PHENIXphasing
HKL-2000data scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B1V

2b1v


Resolution: 2.4→47.131 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 816 5.11 %
Rwork0.1969 15145 -
obs0.1995 15961 81.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.36 Å2 / Biso mean: 69.8059 Å2 / Biso min: 22.96 Å2
Refinement stepCycle: final / Resolution: 2.4→47.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3733 0 64 40 3837
Biso mean--60.74 49.5 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043867
X-RAY DIFFRACTIONf_angle_d0.8055243
X-RAY DIFFRACTIONf_chiral_restr0.053627
X-RAY DIFFRACTIONf_plane_restr0.003646
X-RAY DIFFRACTIONf_dihedral_angle_d15.621409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.54860.3405690.2592109636
2.5486-2.74530.31231100.2407218171
2.7453-3.02160.27911490.2451280892
3.0216-3.45870.29361680.2233293795
3.4587-4.35710.22011600.1739306999
4.35710.20921600.1749305497
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)
16.5726-0.1465.29738.2740.46777.957-0.0786-0.09820.1514-0.17180.6173-1.26820.7662.4076-0.60490.48530.10690.11450.9990.00590.775323.60250.640728.7946
23.84260.5163-1.65975.1310.17235.32610.13461.30390.2995-1.0115-0.01951.0563-0.7974-0.9092-0.00710.64110.0017-0.13610.96740.09530.5428-1.02078.232810.3199
34.04660.1672-0.93165.6643-0.92939.1346-0.2810.1579-0.6478-0.0641-0.0052-0.02631.0594-0.260.28320.4145-0.05560.06720.3602-0.05570.41534.2084-2.527522.6369
49.7591-0.4386-1.5079.63220.8067.6816-0.50330.66820.8597-0.47250.34550.3719-1.9916-0.610.04990.60420.027-0.0760.51120.07780.36530.327515.191218.111
56.7588-1.1412-4.07164.7767-4.19059.0613-0.24720.3461-0.6938-0.11381.24121.3293-0.6923-2.3569-1.00870.67320.3041-0.14821.41250.11230.8256-13.043112.547321.0334
62.43071.95954.22612.71821.91436.2822-0.8141-0.75721.74-0.06740.17750.9718-1.3549-0.94510.60830.63770.12610.00070.5327-0.01720.5882-1.65815.032929.3644
75.9123-1.36790.72944.52672.18459.50230.00040.06130.0963-0.1145-0.11710.0098-0.30611.08630.13120.3182-0.0093-0.01550.47590.04810.357912.07336.882230.7137
83.5890.967-2.24633.55992.36414.8295-0.6598-1.0689-1.02411.3674-0.32860.08952.7868-0.46171.12131.6713-0.04210.33621.17510.01520.71815.9988-11.907739.2369
95.70670.11930.4448.49941.96648.569-0.26010.2386-0.29570.67540.2522-0.86090.67390.97520.11680.36140.0845-0.02260.65940.06520.403817.9161.244338.6728
107.49850.46081.05696.0016-0.1197.89620.271-0.2207-0.00710.2806-0.36560.16520.1084-0.42060.15430.3726-0.0260.03690.3480.03350.24981.92316.953335.7682
118.8388-4.3134-0.59163.9473-0.1683.57540.3587-2.02710.15040.2765-0.32820.49490.1683-1.1815-0.21210.6858-0.3736-0.07271.1751-0.23961.2336-7.1186-7.639820.6928
122.0154-3.95174.57862.02571.00938.5249-0.64330.5726-2.976-0.6531.0297-0.00261.18811.1751-0.40031.11830.16760.17290.6046-0.21530.99026.6676-14.855618.923
136.62711.7491-1.66497.2441-5.20068.08521.0378-0.98510.86712.0923-0.8627-0.0733-0.61240.8281-0.08840.7727-0.2048-0.03920.6213-0.13270.49485.688116.756759.6934
145.87312.29042.17319.71360.86615.2311-0.2611-0.7861-0.61310.1817-0.52891.14270.4755-0.54550.78660.6777-0.12950.20660.5694-0.11120.5241-12.9816-5.105661.1114
154.65650.0448-1.45110.8945-2.58245.6939-0.24130.1356-0.0669-0.27660.0256-0.0008-0.1176-0.70730.17050.4488-0.02870.04420.3731-0.08350.3255-12.19885.81554.6348
165.94360.1726-0.36745.5784-0.77966.14550.00930.31080.0661-0.2918-0.2020.18150.282-0.18830.13860.3965-0.07790.0480.361-0.05480.3014-6.70635.266949.9502
174.2654-1.3273-0.50151.7203-1.08374.5271-0.36110.2424-1.479-0.07290.03690.57942.2649-0.31820.2781.1669-0.06830.24050.4308-0.00920.869-8.5592-13.573153.1652
182.39856.58025.58972.85841.92626.40810.34170.2536-1.52650.4486-0.2714-0.37271.72960.1675-0.03560.90270.03970.14050.4886-0.06390.6059-0.2667-9.356547.4072
199.1905-0.6249-5.40275.90080.51167.97490.07680.2287-0.02450.277-0.14930.1822-0.39130.35610.1470.4016-0.1163-0.00560.3217-0.01770.33992.60037.602250.1204
205.8942-0.702-0.44665.7718-1.63885.0105-0.2596-0.70270.60781.0598-0.2312-0.6387-0.80780.6250.41750.5219-0.172-0.12470.5596-0.05040.468711.118212.802651.4458
219.88751.544-2.76654.114-0.33444.4906-0.12130.1406-0.67770.0196-0.0431-0.05890.44570.04930.1280.4419-0.01170.01790.2992-0.00110.23672.25390.738643.0076
222.60150.15211.95012.00997.51926.8218-0.31590.8127-0.91761.29270.23742.58420.9896-0.9768-0.09181.1387-0.32740.08131.02480.04210.7897-23.8626-3.580147.6102
238.16742.28455.82768.86141.38494.2047-1.16552.2861-0.8369-1.4320.31751.1509-0.33172.22470.10780.6826-0.2057-0.04791.3628-0.09310.803-18.97596.279742.0638
245.97982.61182.08515.77492.24971.98880.0952-0.85031.68981.1845-0.6411.1418-1.5012-2.55460.36890.86850.13340.07950.9295-0.03091.0864-18.553416.496754.3796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 306 through 321 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 393 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 411 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 412 through 421 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 437 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 438 through 455 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 456 through 467 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 468 through 497 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 498 through 527 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 528 through 548 )A0
12X-RAY DIFFRACTION12chain 'C' and (resid 688 through 696 )C0
13X-RAY DIFFRACTION13chain 'B' and (resid 306 through 321 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 322 through 338 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 339 through 371 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 372 through 397 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 398 through 420 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 421 through 437 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 438 through 473 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 474 through 496 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 497 through 527 )B0
22X-RAY DIFFRACTION22chain 'B' and (resid 528 through 537 )B0
23X-RAY DIFFRACTION23chain 'B' and (resid 538 through 551 )B0
24X-RAY DIFFRACTION24chain 'D' and (resid 688 through 697 )D0

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