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

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Basic information

Entry
Database: PDB / ID: 5tnb
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (L372S,L536S) in Complex with the OBHS-BSC, 4-bromophenyl (1R,2R,4S)-6-(4-(2-(dimethylamino)ethoxy)phenyl)-5-(4-hydroxyphenyl)-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 / regulation of branching involved in prostate gland morphogenesis / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / 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 / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / 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 / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 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 / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / Nuclear hormones receptors DNA-binding region signature. ...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-7EB / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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)119,6408
Polymers117,2944
Non-polymers2,3464
Water9,296516
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8204
Polymers58,6472
Non-polymers1,1732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-8 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8204
Polymers58,6472
Non-polymers1,1732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-13 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.549, 58.627, 94.304
Angle α, β, γ (deg.)86.500, 75.020, 62.830
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-7EB / 4-bromophenyl (1S,2R,4S)-6-{4-[2-(dimethylamino)ethoxy]phenyl}-5-(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2-sulfonate


Mass: 586.494 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H28BrNO6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.16 Å3/Da / Density % sol: 43.17 % / Mosaicity: 0.392 °
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: 2.08→50 Å / Num. obs: 53505 / % possible obs: 90.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.076 / Χ2: 0.918 / Net I/av σ(I): 19.106 / Net I/σ(I): 6.6 / Num. measured all: 203042
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.08-2.123.70.358188.8
2.12-2.153.60.272186.3
2.15-2.23.70.233179.6
2.2-2.243.70.253192.8
2.24-2.293.80.206193.6
2.29-2.343.80.182192.9
2.34-2.43.80.168193.2
2.4-2.473.80.152192
2.47-2.543.80.138192.4
2.54-2.623.80.13191.8
2.62-2.713.80.124189.5
2.71-2.823.80.107180.4
2.82-2.953.80.098193.4
2.95-3.113.80.09194.8
3.11-3.33.80.085194.7
3.3-3.563.80.078192.7
3.56-3.913.80.07190.1
3.91-4.483.80.061185.8
4.48-5.643.90.056194.9
5.64-503.90.034190.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1690refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→46.637 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.15 / Phase error: 22.5
RfactorNum. reflection% reflection
Rfree0.2178 1912 3.71 %
Rwork0.1875 --
obs0.1887 51520 87.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 228.55 Å2 / Biso mean: 40.1724 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: final / Resolution: 2.08→46.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7045 0 148 516 7709
Biso mean--65.07 43.28 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027368
X-RAY DIFFRACTIONf_angle_d0.5889991
X-RAY DIFFRACTIONf_chiral_restr0.0211176
X-RAY DIFFRACTIONf_plane_restr0.0021227
X-RAY DIFFRACTIONf_dihedral_angle_d142714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0786-2.13060.25921060.22323126323277
2.1306-2.18820.25941140.21833073318776
2.1882-2.25260.36071480.29133423357183
2.2526-2.32530.25661110.21463518362986
2.3253-2.40840.24161620.23582374490
2.4084-2.50490.19731550.19193626378190
2.5049-2.61890.21781240.19793647377189
2.6189-2.75690.24221420.2073485362785
2.7569-2.92960.27481440.19753505364986
2.9296-3.15580.21381370.19673838397595
3.1558-3.47320.21191460.19013792393893
3.4732-3.97560.18831420.15873628377089
3.9756-5.00790.17571310.15263667379890
5.0079-46.64910.19741500.17973698384891
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)
15.1364-1.39930.66264.8295-1.35122.2258-0.07750.34660.8990.2708-0.3322-0.6463-0.22130.24940.3650.2335-0.07210.00740.24560.00460.1751-4.019226.1682-38.7307
27.8617-4.73960.38425.9067-0.42712.5068-0.05880.5565-0.3006-0.2345-0.1970.0853-0.3146-0.00470.26550.2804-0.08040.00520.2066-0.02260.1977-9.597527.2517-46.2547
32.2785-0.7594-1.11163.59120.38934.31420.07-0.04760.11310.019-0.00560.0307-0.0892-0.0298-0.01240.1477-0.043-0.00950.14280.00690.2065-9.728820.4054-41.4168
43.2626-0.90040.21463.72610.27663.2699-0.108-0.3090.21440.2847-0.00150.2261-0.0747-0.1130.08560.2046-0.03240.01970.1483-0.00770.2635-10.978915.7333-32.9156
53.3985-3.7819-1.81726.08054.86455.2352-0.62610.8838-0.4485-1.1724-0.92430.72341.4518-0.61381.12180.7947-0.1380.22240.4353-0.17390.5405-5.67513.6674-52.3145
62.84050.5720.56553.7350.7892.15880.08790.24160.0387-0.43230.2715-0.40180.10640.7122-0.37620.19940.00130.03160.29810.01130.26833.07834.6004-38.5699
75.5584-0.58493.34544.6492-1.63354.9883-0.22380.03810.0318-0.13540.26630.4582-0.181-0.2789-0.1180.1328-0.03930.04520.168-0.01390.224-13.12449.0929-35.7557
83.4105-2.8161-1.49062.68832.38094.45790.461.24180.9998-0.82650.04540.6503-0.586-0.2373-0.61920.49720.0820.01140.35070.14610.4582-7.668621.7257-56.924
94.91330.75323.32922.61540.77472.7099-0.11350.1154-0.021-0.0689-0.00190.34480.2656-0.09690.04930.3686-0.11230.06080.26050.04450.3252-23.42-15.1806-38.1415
104.19530.60751.75044.08191.21994.41010.2002-0.12720.18220.0080.00090.58450.1493-0.5024-0.10260.2313-0.09130.05380.25680.02020.3499-29.4563-8.0348-38.2977
113.80720.41120.34943.60010.21542.747-0.07070.3467-0.0051-0.32390.05870.19180.1714-0.1266-0.00530.2158-0.08210.00080.17820.01650.2037-18.4051-5.6662-44.8087
123.71620.63170.33493.0557-0.34453.2601-0.0435-0.04680.16370.06230.00520.34110.1884-0.3360.0350.1698-0.04160.06730.121-0.02640.2141-16.4118-0.9756-35.6199
134.52441.9411-0.33534.9052-1.13332.8496-0.05280.0264-0.84-0.2878-0.1478-0.80180.27720.24940.11670.21960.11970.00670.2535-0.03420.2126-4.12952.2118-86.8228
141.95891.2670.09053.58780.14522.7092-0.0315-0.0091-0.04360.0617-0.0254-0.01460.06870.02030.02270.18550.0652-0.00230.1749-0.00360.205-8.62486.5909-81.5296
156.7417-4.8976-2.02155.2776-1.71046.62850.6215-0.1364-0.0193-0.9943-0.05351.39-0.1537-2.0328-0.28810.50250.0072-0.28120.43940.00660.8797-22.0874-1.2535-90.8549
163.80930.66770.5044.634-0.06274.1827-0.18510.3501-0.2442-0.5970.01740.33250.124-0.10170.17110.2680.0299-0.03090.1578-0.00990.2698-11.14812.6377-92.6791
172.41884.73063.00399.75377.56279.4236-0.378-0.51430.36450.8866-0.74950.6241-0.6724-0.52371.04470.5170.08-0.08870.4154-0.00850.6346-5.448425.0451-72.9418
182.5814-0.38670.24664.3906-0.17897.92690.0554-0.01680.19130.25990.1132-0.6161-0.20490.8964-0.27050.15610.00870.01940.29360.04290.37823.020823.6932-87.1649
194.4760.6866-3.34945.5322-3.02957.5534-0.341-0.0858-0.2555-0.2670.08050.35590.4916-0.11950.20640.12640.0249-0.04080.1553-0.03260.2252-13.088719.3013-90.2967
207.6505-0.52720.8846.288-0.10225.58480.0324-0.9535-0.66350.98580.11170.66050.3141-0.7391-0.17020.4664-0.08390.04240.38580.02110.3035-8.82016.9355-68.8015
213.2246-0.556-1.95462.91851.6022.9327-0.06110.0830.1347-0.1603-0.0550.3661-0.3736-0.15280.04580.30360.0392-0.04770.22120.0560.2343-22.582943.4136-88.8253
222.8573-0.3487-0.11693.42391.64312.342-0.1049-0.2140.0110.14710.0360.2446-0.1997-0.25030.05930.22010.06170.00160.18190.03190.1947-25.335535.7791-83.5916
233.48170.39871.3782.4472-0.10945.83840.0474-0.2238-0.1620.49620.063-0.06670.1102-0.0655-0.06870.26470.0644-0.00670.12930.00470.1807-16.027731.1386-82.4113
243.5323-0.17260.96562.62180.29994.4384-0.13310.04940.0601-0.01040.02390.0997-0.1638-0.2940.08270.13870.02960.00410.11220.00920.1538-16.886428.7623-91.7459
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 306 through 338 )A306 - 338
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 363 )A339 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 421 )A364 - 421
4X-RAY DIFFRACTION4chain 'A' and (resid 422 through 455 )A422 - 455
5X-RAY DIFFRACTION5chain 'A' and (resid 456 through 465 )A456 - 465
6X-RAY DIFFRACTION6chain 'A' and (resid 466 through 496 )A466 - 496
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 526 )A497 - 526
8X-RAY DIFFRACTION8chain 'A' and (resid 527 through 546 )A527 - 546
9X-RAY DIFFRACTION9chain 'B' and (resid 305 through 341 )B305 - 341
10X-RAY DIFFRACTION10chain 'B' and (resid 342 through 371 )B342 - 371
11X-RAY DIFFRACTION11chain 'B' and (resid 372 through 472 )B372 - 472
12X-RAY DIFFRACTION12chain 'B' and (resid 473 through 546 )B473 - 546
13X-RAY DIFFRACTION13chain 'C' and (resid 306 through 338 )C306 - 338
14X-RAY DIFFRACTION14chain 'C' and (resid 339 through 405 )C339 - 405
15X-RAY DIFFRACTION15chain 'C' and (resid 406 through 421 )C406 - 421
16X-RAY DIFFRACTION16chain 'C' and (resid 422 through 455 )C422 - 455
17X-RAY DIFFRACTION17chain 'C' and (resid 456 through 465 )C456 - 465
18X-RAY DIFFRACTION18chain 'C' and (resid 466 through 496 )C466 - 496
19X-RAY DIFFRACTION19chain 'C' and (resid 497 through 525 )C497 - 525
20X-RAY DIFFRACTION20chain 'C' and (resid 526 through 546 )C526 - 546
21X-RAY DIFFRACTION21chain 'D' and (resid 305 through 341 )D305 - 341
22X-RAY DIFFRACTION22chain 'D' and (resid 342 through 411 )D342 - 411
23X-RAY DIFFRACTION23chain 'D' and (resid 412 through 465 )D412 - 465
24X-RAY DIFFRACTION24chain 'D' and (resid 466 through 546 )D466 - 546

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