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- PDB-5tn9: Crystal Structure of the ER-alpha Ligand-binding Domain (L372S,L5... -

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Basic information

Entry
Database: PDB / ID: 5tn9
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (L372S,L536S) in Complex with the OBHS-BSC, 4-bromophenyl (1R,2R,4S)-5-(4-hydroxyphenyl)-6-(4-(2-(piperidin-1-yl)ethoxy)phenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate
ComponentsEstrogen receptor
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 / 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 ...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 / 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 / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / 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 / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / Nuclear Receptor transcription pathway / response to estrogen / 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 / PIP3 activates AKT signaling / response to estradiol / 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 / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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-7EC / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.253 Å
AuthorsNwachukwu, J.C. / Sharma, N. / Carlson, K.E. / Srinivasan, S. / Sharma, A. / Katzenellenbogen, J.A. / Nettles, K.W.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Exploring the Structural Compliancy versus Specificity of the Estrogen Receptor Using Isomeric Three-Dimensional Ligands.
Authors: Sharma, N. / Carlson, K.E. / Nwachukwu, J.C. / Srinivasan, S. / Sharma, A. / Nettles, K.W. / Katzenellenbogen, J.A.
History
DepositionOct 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 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: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8008
Polymers117,2944
Non-polymers2,5064
Water5,657314
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9004
Polymers58,6472
Non-polymers1,2532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-9 kcal/mol
Surface area18310 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9004
Polymers58,6472
Non-polymers1,2532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-11 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.430, 58.560, 93.770
Angle α, β, γ (deg.)80.27, 75.04, 62.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29323.469 Da / Num. of mol.: 4 / Fragment: ligand-binding domain / Mutation: L372S, L536S
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: Chemical
ChemComp-7EC / 4-bromophenyl (1S,2R,4S)-5-(4-hydroxyphenyl)-6-{4-[2-(piperidin-1-yl)ethoxy]phenyl}-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 626.558 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H32BrNO6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.15 Å3/Da / Density % sol: 42.69 % / Mosaicity: 0.419 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 14, 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.253→50 Å / Num. obs: 42008 / % possible obs: 91.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/av σ(I): 15.086 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.26-2.33.70.352193.1
2.3-2.343.70.317193.4
2.34-2.393.70.303193
2.39-2.433.70.251191.9
2.43-2.493.80.237192.3
2.49-2.553.70.216192.4
2.55-2.613.80.191191.5
2.61-2.683.80.169190.2
2.68-2.763.80.16187.3
2.76-2.853.80.129178
2.85-2.953.80.111194.4
2.95-3.073.80.097195.5
3.07-3.213.80.085194.3
3.21-3.383.80.075193.7
3.38-3.593.90.065192.7
3.59-3.863.80.061189
3.86-4.253.70.053182.3
4.25-4.873.90.049196
4.87-6.133.90.052193.6
6.13-503.90.038189.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.253→46.292 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 23.97
RfactorNum. reflection% reflection
Rfree0.2381 1867 4.76 %
Rwork0.2068 --
obs0.2083 39190 85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.253→46.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 135 314 7211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027064
X-RAY DIFFRACTIONf_angle_d0.5649588
X-RAY DIFFRACTIONf_dihedral_angle_d14.6432586
X-RAY DIFFRACTIONf_chiral_restr0.021150
X-RAY DIFFRACTIONf_plane_restr0.0021169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2529-2.31380.2522940.24131759X-RAY DIFFRACTION52
2.3138-2.38180.28371260.24452673X-RAY DIFFRACTION80
2.3818-2.45870.30711450.23592901X-RAY DIFFRACTION86
2.4587-2.54660.28131610.23072974X-RAY DIFFRACTION87
2.5466-2.64850.26061510.22452907X-RAY DIFFRACTION86
2.6485-2.76910.241450.22642800X-RAY DIFFRACTION84
2.7691-2.9150.23021370.21732824X-RAY DIFFRACTION83
2.915-3.09760.2891540.21143154X-RAY DIFFRACTION94
3.0976-3.33680.24041460.21173156X-RAY DIFFRACTION93
3.3368-3.67240.19551610.19613081X-RAY DIFFRACTION91
3.6724-4.20350.18861420.17412828X-RAY DIFFRACTION84
4.2035-5.29480.24421640.18263233X-RAY DIFFRACTION95
5.2948-46.30190.22361410.21313033X-RAY DIFFRACTION90
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)
12.09640.5082-0.17432.99240.55842.0793-0.0757-0.02960.21440.0112-0.00540.11-0.0936-0.10410.12460.16970.0856-0.01170.15140.02210.14598.341922.478742.2951
25.1260.0901-0.14322.93140.15814.1279-0.1620.09780.1577-0.22240.0173-0.21390.08510.14990.07070.11620.0591-0.00060.06130.00860.215412.154713.597235.5723
31.93630.4207-0.74373.6496-0.01482.55440.1033-0.1332-0.00170.3993-0.04640.00350.1708-0.27720.00480.09770.08750.00540.04280.02190.18316.06828.718340.3053
43.2038-0.5861.67092.4423-0.43585.8799-0.10340.3258-0.0869-0.4627-0.0167-0.52150.23520.4358-0.00230.40660.06190.07130.2013-0.0690.224621.7394-14.42533.3752
53.0982-1.37620.52283.6721-0.43811.8958-0.1218-0.03260.17280.10660.0425-0.3250.17570.080.07030.17870.020.0480.1017-0.0010.132918.4377-5.874740.1082
61.3436-0.4847-0.91311.7815-0.52721.7805-0.3164-0.33530.74030.1572-0.7065-0.5041-0.12650.43710.09630.08720.09350.10390.91880.0610.977635.62580.188441.2785
71.7587-0.33960.04564.17170.60052.4597-0.0312-0.044-0.15170.1180.0334-0.00790.1423-0.07340.0030.125-0.0666-0.00280.14520.02490.19039.74095.24586.056
84.2142-1.27393.97160.6716-1.30093.75830.8116-0.3662-0.0513-0.8253-0.08260.16240.6310.2642-0.79961.0638-0.2350.04460.6331-0.12610.60416.015824.922872.0354
91.5999-0.30080.50544.34691.19992.60620.07240.24510.201-0.3265-0.03370.1565-0.1285-0.2158-0.02560.1503-0.0669-0.01270.17960.05750.21666.947516.894685.6854
103.50060.1247-0.16763.5561-0.74131.4037-0.1880.21630.0228-0.17770.171-0.3301-0.30060.3758-0.00330.2161-0.129-0.01580.1407-0.01030.125524.739335.224584.4287
111.49050.618-1.32272.11950.78762.0412-0.03980.0052-0.1378-0.16350.04040.2907-0.1483-0.01730.01510.176-0.0595-0.02250.1707-0.01380.120616.423329.1788.1978
122.98951.15550.76183.3706-0.75053.6399-0.1244-0.1363-0.20110.08860.0192-0.0663-0.3060.1864-0.02170.0834-0.0418-0.00950.0852-0.01090.128917.26527.617391.0447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 306:411)
2X-RAY DIFFRACTION2(chain A and resid 412:461)
3X-RAY DIFFRACTION3(chain A and resid 468:546)
4X-RAY DIFFRACTION4(chain B and resid 305:342)
5X-RAY DIFFRACTION5(chain B and resid 343:522)
6X-RAY DIFFRACTION6(chain B and resid 523:546)
7X-RAY DIFFRACTION7(chain C and resid 307:458)
8X-RAY DIFFRACTION8(chain C and resid 459:467)
9X-RAY DIFFRACTION9(chain C and resid 468:546)
10X-RAY DIFFRACTION10(chain D and resid 305:425)
11X-RAY DIFFRACTION11(chain D and resid 426:469)
12X-RAY DIFFRACTION12(chain D and resid 470:546)

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