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- PDB-7rnm: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

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Basic information

Entry
Database: PDB / ID: 7rnm
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with 2-(2-Chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)isoindolin-5-ol and GRIP Peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Breast Cancer / Estrogen Receptor / Alpha Helical Bundle
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 / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / 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 / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / nuclear receptor coactivator activity / 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 / transcription coactivator binding / beta-catenin 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 / protein dimerization activity / 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
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, receptor-binding domain ...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, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / : / 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 / 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
Similarity search - Domain/homology
Chem-61Z / Nuclear receptor coactivator 2 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJoiner, C. / Sammeta, V.K.R. / Norris, J.D. / McDonnell, D.P. / Willson, T.M. / Fanning, S.W.
CitationJournal: Helv.Chim.Acta / Year: 2023
Title: Structural Determinants of the Binding and Activation of Estrogen Receptor alpha by Phenolic Thieno[2,3-d]pyrimidines
Authors: Reddy Sammeta, V. / Anderson, B.M. / Norris, J.D. / Torrice, C.D. / Joiner, C. / Liu, S. / Li, H. / Popov, K.I. / Fanning, S.W. / McDonnell, D.P. / Willson, T.M.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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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)60,1946
Polymers59,4344
Non-polymers7602
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-27 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.094, 83.456, 58.420
Angle α, β, γ (deg.)90.000, 108.520, 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: 28440.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 1276.530 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2 / Production host: synthetic construct (others) / References: UniProt: E7EWM1
#3: Chemical ChemComp-61Z / 2-(2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-isoindol-5-ol


Mass: 379.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14ClN3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39739 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 1 / Net I/σ(I): 3785
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1935 / CC1/2: 0.576

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D0F

6d0f


Resolution: 1.9→46.44 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1804 5 %
Rwork0.1854 34262 -
obs0.1872 36066 90.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.54 Å2 / Biso mean: 27.0684 Å2 / Biso min: 5.8 Å2
Refinement stepCycle: final / Resolution: 1.9→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 52 378 3994
Biso mean--29.98 33.87 -
Num. residues----465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.960.3648620.2735990105235
1.96-2.010.3187770.24781704178158
2.01-2.080.24591410.21452522266387
2.08-2.150.26141400.20122759289995
2.15-2.240.23731520.19182889304199
2.24-2.340.19261510.188728953046100
2.34-2.460.25221660.179828953061100
2.46-2.620.23331570.183229093066100
2.62-2.820.2331300.191329643094100
2.82-3.10.22871590.181529203079100
3.11-3.550.20461480.179929053053100
3.55-4.480.19631470.159429583105100
4.48-46.440.19661740.18932952312699
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)
12.8298-0.62710.61691.3654-1.02353.36680.0252-0.57720.19840.33760.0057-0.1146-0.30060.28860.31660.0679-0.0523-0.05310.2999-0.03760.160422.37056.621523.0944
22.1912-0.13751.29971.499-0.32481.7514-0.1208-0.187-0.2996-0.04450.11490.0510.0727-0.03090.01850.0970.00840.01040.11330.00880.05157.6403-1.334114.0347
36.70214.97581.85773.75131.01252.88430.09950.1017-0.2459-0.1919-0.15160.1332-0.2408-0.1747-0.03250.09210.060.01030.212-0.01220.2971-12.41616.439717.4412
45.4377-0.34025.7535.1026-2.35997.43820.18580.4942-0.964-1.05330.3482-0.06010.7791-0.1307-0.37180.6131-0.18210.04740.2729-0.06030.30118.555-14.314-10.6423
52.6785-1.6573-3.24035.64483.02726.32820.09430.0230.9510.326-0.17320.2387-0.7394-0.6417-0.06060.29390.04520.10760.1805-0.04370.3731-5.711918.192626.2418
64.20090.48431.60311.69440.17372.4459-0.05790.1924-0.5519-0.37230.2915-0.21190.08480.2783-0.07560.2298-0.01540.07560.3746-0.03130.186523.7506-0.8349-6.7403
73.19970.86880.69642.43790.56862.7313-0.0560.1513-0.224-0.22610.07970.09080.261-0.0118-0.01660.2424-0.03140.03730.1131-0.01690.090311.5161-3.3574-6.221
80.75130.7502-0.51131.4257-1.30363.092-0.11510.18690.3252-0.00910.19220.1714-0.7563-0.3022-0.33240.6965-0.0033-0.08920.22540.08130.20089.361916.312-8.3488
96.0334-0.37161.92543.1818-0.66483.8541-0.5171-0.15070.78230.61440.26590.1781-0.8578-0.22650.18350.45710.101-0.02830.15440.0060.250110.933814.64292.3563
103.5369-0.81471.45311.7780.82033.6545-0.05060.0823-0.1995-0.0784-0.0119-0.10830.1860.2530.0430.0806-0.00270.03630.1498-0.01850.102822.7719-1.78125.6445
114.89271.01891.77332.3090.57883.0863-0.2360.17710.2545-0.1570.05090.1691-0.2042-0.1810.19060.08710.01730.01720.10550.00490.05910.32284.84376.2583
122.21380.28150.7221.98570.10460.5910.1955-0.1113-0.29190.3537-0.14520.2029-0.1989-0.5365-0.07170.3845-0.0913-0.09580.42710.06230.3488-2.6865-4.081-9.1954
134.911.21170.00341.69360.2311.61970.0696-0.52720.37310.2703-0.06520.21560.00780.2133-0.04110.23840.01570.00970.1872-0.02850.11363.8651.301431.8372
146.93414.93061.33456.4671.50642.80950.1703-0.2328-0.09710.2564-0.11450.1842-0.1133-0.315-0.00910.08560.02440.04020.1307-0.00210.1421-5.18213.020727.0752
152.03630.369-0.26713.40960.00922.37010.0824-0.0378-0.04050.1202-0.06330.02430.04820.00230.02060.03850.00830.02370.0776-0.00010.08140.8086-0.283922.8238
163.0116-0.03193.59345.8904-0.09365.93790.03930.4572-0.3254-0.3221-0.1216-0.08910.30570.07780.01790.16230.00450.02870.1046-0.02510.14914.9146-10.750617.5795
173.52770.6045-0.37545.1552-0.21843.72930.028-0.1820.14870.13630.0836-0.1791-0.36440.2267-0.08290.0394-0.02530.03570.1047-0.03750.084912.20254.780521.3011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 474 through 496 )B474 - 496
2X-RAY DIFFRACTION2chain 'B' and (resid 497 through 530 )B497 - 530
3X-RAY DIFFRACTION3chain 'B' and (resid 531 through 547 )B531 - 547
4X-RAY DIFFRACTION4chain 'C' and (resid 688 through 695 )C688 - 695
5X-RAY DIFFRACTION5chain 'D' and (resid 688 through 696 )D688 - 696
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 340 )A307 - 340
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 394 )A341 - 394
8X-RAY DIFFRACTION8chain 'A' and (resid 395 through 421 )A395 - 421
9X-RAY DIFFRACTION9chain 'A' and (resid 422 through 438 )A422 - 438
10X-RAY DIFFRACTION10chain 'A' and (resid 439 through 496 )A439 - 496
11X-RAY DIFFRACTION11chain 'A' and (resid 497 through 530 )A497 - 530
12X-RAY DIFFRACTION12chain 'A' and (resid 531 through 547 )A531 - 547
13X-RAY DIFFRACTION13chain 'B' and (resid 307 through 338 )B307 - 338
14X-RAY DIFFRACTION14chain 'B' and (resid 339 through 363 )B339 - 363
15X-RAY DIFFRACTION15chain 'B' and (resid 364 through 420 )B364 - 420
16X-RAY DIFFRACTION16chain 'B' and (resid 421 through 437 )B421 - 437
17X-RAY DIFFRACTION17chain 'B' and (resid 438 through 473 )B438 - 473

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