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- PDB-5u2d: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 5u2d
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in complex with Oxabicyclic Heptene Sulfonate (OBHS)
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / protein ligand complex
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / Developmental Lineage of Mammary Gland Alveolar Cells / locomotor rhythm / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of glucose metabolic process ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / steroid hormone receptor signaling pathway / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / Developmental Lineage of Mammary Gland Alveolar Cells / locomotor rhythm / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of glucose metabolic process / negative regulation of smooth muscle cell apoptotic process / Synthesis of bile acids and bile salts / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / regulation of lipid metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Nuclear signaling by ERBB4 / estrogen receptor signaling pathway / Recycling of bile acids and salts / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / cellular response to hormone stimulus / positive regulation of nitric-oxide synthase activity / steroid binding / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / stem cell differentiation / protein localization to chromatin / positive regulation of adipose tissue development / bile acid and bile salt transport / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 14-3-3 protein binding / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / ESR-mediated signaling / negative regulation of smoothened signaling pathway / negative regulation of miRNA transcription / TBP-class protein binding / nuclear estrogen receptor binding / nitric-oxide synthase regulator activity / nuclear receptor binding / transcription corepressor binding / negative regulation of canonical NF-kappaB signal transduction / transcription coregulator binding / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / euchromatin / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / response to estrogen / beta-catenin binding / mRNA transcription by RNA polymerase II / nuclear receptor activity / transcription coactivator binding / positive regulation of nitric oxide biosynthetic process / transcription coregulator activity / Constitutive Signaling by Aberrant PI3K in Cancer / sequence-specific double-stranded DNA binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / positive regulation of cytosolic calcium ion concentration / HATs acetylate histones / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / transcription coactivator activity / Extra-nuclear estrogen signaling / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / protein domain specific binding / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / protein kinase binding
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-OBH / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsNwachukwu, J.C. / Erumbi, R. / Nowak, J. / Carlson, K.E. / Katzenellenbogen, J.A. / Izard, T. / Nettles, K.W.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells.
Authors: Stender, J.D. / Nwachukwu, J.C. / Kastrati, I. / Kim, Y. / Strid, T. / Yakir, M. / Srinivasan, S. / Nowak, J. / Izard, T. / Rangarajan, E.S. / Carlson, K.E. / Katzenellenbogen, J.A. / Yao, X. ...Authors: Stender, J.D. / Nwachukwu, J.C. / Kastrati, I. / Kim, Y. / Strid, T. / Yakir, M. / Srinivasan, S. / Nowak, J. / Izard, T. / Rangarajan, E.S. / Carlson, K.E. / Katzenellenbogen, J.A. / Yao, X.Q. / Grant, B.J. / Leong, H.S. / Lin, C.Y. / Frasor, J. / Nettles, K.W. / Glass, C.K.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 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)62,6366
Polymers61,7594
Non-polymers8772
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-36 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.700, 81.360, 58.360
Angle α, β, γ (deg.)90.000, 111.070, 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 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-OBH / cyclohexa-2,5-dien-1-yl (1S,2R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 438.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 37.31 % / Mosaicity: 1.334 °
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: NSLS / Beamline: X12C / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: Channel-cut Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→26.61 Å / Num. obs: 55884 / % possible obs: 97.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.86 Å2 / Rmerge(I) obs: 0.082 / Χ2: 2.856 / Net I/av σ(I): 22.303 / Net I/σ(I): 8 / Num. measured all: 186459
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
1.65-1.681.9178.7
1.68-1.712185.6
1.71-1.742.2191.5
1.74-1.782.6194.7
1.78-1.823198
1.82-1.863.3199
1.86-1.93.5199.9
1.9-1.963.6199.90.76
1.96-2.013.711000.633
2.01-2.083.7199.90.476
2.08-2.153.6199.90.643
2.15-2.243.711000.288
2.24-2.343.7199.90.227
2.34-2.463.711000.184
2.46-2.623.711000.154
2.62-2.823.7199.90.128
2.82-3.113.7199.90.104
3.11-3.553.6199.90.077
3.55-4.483.5199.70.051
4.48-503.7197.70.042

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.3refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→26.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.139
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1946 5.08 %RANDOM
Rwork0.169 ---
obs0.171 38270 95.4 %-
Displacement parametersBiso max: 122.27 Å2 / Biso mean: 38.09 Å2 / Biso min: 11.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.133 Å20 Å2-2.4142 Å2
2---2.9084 Å20 Å2
3---3.0414 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 1.86→26.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 62 347 4429
Biso mean--26.25 44.54 -
Num. residues----508
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1512SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it4253HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion543SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5411SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4253HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5775HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion16.43
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.289 141 5.43 %
Rwork0.237 2454 -
all-2595 -
obs--84.01 %
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)
11.1044-0.62921.16532.27911.08877.2007-0.06320.0753-0.03280.13710.01770.09410.1056-0.01850.0456-0.04910.06580.1035-0.10080.0554-0.1481-20.693621.04758.0787
22.5169-0.7795-0.69531.75290.89894.3394-0.1659-0.325-0.04940.08950.1172-0.036-0.04540.31050.0488-0.0470.03270.0674-0.07470.0143-0.1468-11.729319.0785.3413
33.1474-0.8703-0.24351.15870.13094.39720.0011-0.03760.2112-0.23280.024-0.0272-0.3744-0.0874-0.0250.00140.02310.0753-0.1082-0.0015-0.1036-15.033723.7929-4.0088
42.0924-0.1675-0.19590.7892-0.33193.2076-0.07710.1416-0.0766-0.00680.07920.1332-0.0675-0.4857-0.0021-0.04610.02160.0789-0.0499-0.0109-0.098-20.676120.5-10.6196
54.7162-0.5918-0.65491.8766-3.3313-1.2046-0.1757-0.2784-0.11590.17120.0985-0.13870.2550.18280.07730.01930.12290.05680.02610.0828-0.05350.28189.77054.1102
6-0.7392-2.33811.7232.66420.04092.5511-0.09730.1370.4148-0.04920.0486-0.0083-0.0110.01370.0487-0.05750.11530.07010.17470.1235-0.06-14.498634.9155-31.4898
70.311-1.2226-0.27643.05051.04250.6763-0.050.3702-0.28410.14660.055-0.10240.4764-0.2709-0.0050.03290.01120.09-0.0017-0.0263-0.04964.78598.4247-33.2622
83.4216-0.6288-0.88991.69450.73042.5141-0.03210.15210.2724-0.09270.0265-0.1677-0.16850.05340.0055-0.04790.00110.0306-0.04970.0094-0.06520.436123.0402-24.7521
90.1578-2.67272.44260.20332.08923.4191-0.01870.1273-0.1653-0.1278-0.03260.08830.1774-0.0570.05130.051-0.11480.1467-0.0072-0.1228-0.0058-6.02666.2794-30.4181
103.31150.96211.17982.43770.46123.594-0.04270.0361-0.5168-0.0601-0.0424-0.05280.4991-0.12040.08510.1143-0.02470.1738-0.1624-0.02260.0445-4.79864.5559-20.7908
116.31880.6196-0.65253.74910.61154.08140.08370.38760.01710.0393-0.00230.0476-0.1789-0.406-0.0814-0.0690.04690.049-0.01050.0138-0.0907-12.582723.6786-22.7115
123.5369-2.4245-1.56754.69940.38593.16080.2530.60050.2639-0.1669-0.1771-0.2119-0.4591-0.3519-0.0759-0.06830.12410.03980.07840.0566-0.1425-20.302630.3392-23.4653
134.9296-0.7665-1.28931.06450.31111.7551-0.2851-0.07930.02180.09870.1074-0.13410.09160.13520.1777-0.01580.02260.0496-0.07430.0097-0.0661-2.340918.0147-15.2332
14-0.28470.22770.31461.5606-3.02250.28470.0237-0.0579-0.1720.0483-0.00450.00280.149-0.0625-0.01920.15870.08480.2627-0.22280.1955-0.0836-15.83350.81747.9942
151.52771.2336-0.8812.4531-0.74850.17560.00320.0230.12040.01950.0018-0.0845-0.10820.0346-0.005-0.079-0.0350.1015-0.02950.08190.06169.446333.5754-24.8332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|305 - A|338 }A305 - 338
2X-RAY DIFFRACTION2{ A|339 - A|420 }A339 - 420
3X-RAY DIFFRACTION3{ A|421 - A|465 }A421 - 465
4X-RAY DIFFRACTION4{ A|466 - A|525 }A466 - 525
5X-RAY DIFFRACTION5{ A|526 - A|553 }A526 - 553
6X-RAY DIFFRACTION6{ B|303 - B|322 }B303 - 322
7X-RAY DIFFRACTION7{ B|323 - B|338 }B323 - 338
8X-RAY DIFFRACTION8{ B|339 - B|394 }B339 - 394
9X-RAY DIFFRACTION9{ B|395 - B|407 }B395 - 407
10X-RAY DIFFRACTION10{ B|408 - B|437 }B408 - 437
11X-RAY DIFFRACTION11{ B|438 - B|472 }B438 - 472
12X-RAY DIFFRACTION12{ B|473 - B|496 }B473 - 496
13X-RAY DIFFRACTION13{ B|497 - B|553 }B497 - 553
14X-RAY DIFFRACTION14{ C|687 - C|697 }C687 - 697
15X-RAY DIFFRACTION15{ D|687 - D|696 }D687 - 696

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