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- PDB-7sfo: Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex wi... -

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Entry
Database: PDB / ID: 7sfo
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with 3-(((2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)amino)methyl)phenol and GRIP Peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Estrogen Receptor / Hormone / Breast Cancer / 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 / 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 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / 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 / negative regulation of miRNA transcription / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / euchromatin / negative regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / regulation of inflammatory response / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / transcription regulator complex / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / 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
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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Ligand-binding domain of nuclear hormone receptor
Similarity search - Domain/homology
Chem-98L / Nuclear receptor coactivator 2 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJoyner, C. / Reddy, V.K. / Wilson, T. / Fanning, S.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha
Authors: Fanning, S.W.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)60,1706
Polymers59,4344
Non-polymers7362
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-30 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.089, 83.286, 58.486
Angle α, β, γ (deg.)90.000, 108.920, 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 / 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) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 1276.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: E7EWM1
#3: Chemical ChemComp-98L / 3-{[(2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methyl}phenol


Mass: 367.852 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14ClN3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8,000, HEPES pH 8.0, 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: MAR CCD 165 mm / Detector: CCD / Date: Sep 29, 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: 40060 / % possible obs: 99.7 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 6612
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 2005 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.18.2-3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CBZ

6cbz


Resolution: 1.9→44.75 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1870 5.02 %
Rwork0.177 --
obs0.1794 37221 92.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.58 Å2 / Biso mean: 26.0865 Å2 / Biso min: 7.18 Å2
Refinement stepCycle: final / Resolution: 1.9→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3633 0 50 391 4074
Biso mean--18.83 33.5 -
Num. residues----466
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)
12.0557-0.38430.54875.2587-0.31472.10450.1086-0.02770.2823-0.1516-0.1243-0.0564-0.34920.0660.0040.0963-0.00580.0580.1106-0.02890.11233.49676.680921.8997
24.13141.3496-0.04743.47750.10093.17620.0203-0.03-0.72680.0815-0.0446-0.070.40240.00350.02540.204-0.01330.06170.1090.00550.245-3.2484-15.513924.0065
32.7738-0.84551.17355.5458-0.55774.1501-0.00740.4331-0.7461-0.029-0.1228-0.08580.1708-0.07180.02350.1472-0.01310.01160.1103-0.03630.2144.5876-13.359817.5947
44.076-0.8048-0.40992.3451-0.19211.63630.0626-0.34680.2090.1607-0.0715-0.135-0.15870.33570.02730.116-0.02540.00340.1809-0.04030.094417.04922.964422.4508
56.15640.29841.30220.9172-0.30581.4006-0.0531-0.062-0.2828-0.07420.0630.01530.0634-0.03680.0010.1070.0040.020.0798-0.00780.06827.4319-3.647113.8955
65.32553.20971.0392.11620.34142.36410.03060.11050.077-0.1486-0.08390.2088-0.3972-0.2685-0.03190.08770.06150.0060.2025-0.05880.2942-12.6364.08617.4702
73.9988-0.67442.46589.22054.37094.23890.4259-0.2674-1.0477-0.2342-0.35420.56121.3717-0.1688-0.01450.4752-0.06030.01870.23920.0170.29877.872-16.3595-10.4982
85.0314-3.3339-1.6292.3995-0.03787.029-0.0604-0.09691.02280.3343-0.4180.2724-0.8114-0.39870.13530.3180.04370.09790.2079-0.08950.4505-6.103916.334426.3593
92.88111.24511.06510.57980.64462.7066-0.19570.901-0.8185-0.50180.3054-0.49510.07020.4841-0.1770.3086-0.090.09760.4454-0.07710.0422.4772-1.8252-7.3141
106.45-0.87733.16032.7758-1.34854.8104-0.42850.35480.1512-0.38270.1970.1699-0.1142-0.05260.23740.3628-0.0822-0.03360.218-0.01720.12717.8461-1.602-11.85
113.77860.30.37262.74920.4272.5866-0.02070.0855-0.47420.04530.04880.0390.36990.0209-0.02160.2211-0.01280.00740.1359-0.02110.092112.4339-7.354-2.1607
121.44151.49750.89131.60851.19172.5644-0.49820.7880.528-1.03140.34210.3815-1.01960.04620.0160.5896-0.0606-0.14320.27270.07710.24827.767714.3682-8.3394
132.5294-0.35522.86923.2582-0.4913.6749-0.41790.04780.88570.09080.01260.1455-0.56990.07750.35090.26630.0186-0.04270.12620.03170.229610.561912.3482.4893
143.8972-1.74261.34992.33031.02424.1863-0.00680.0785-0.18920.1203-0.05850.0065-0.01710.04080.16930.13470.00370.03270.1225-0.00650.073218.4725-2.51542.9169
153.74570.09680.78324.78180.73774.1969-0.08680.1635-0.1545-0.3948-0.0650.10130.46620.2926-0.07290.0970.04750.03260.1958-0.00230.177526.4641-5.57188.1356
162.71710.10022.30672.02980.51324.78140.0131-0.07310.2507-0.0787-0.11610.1905-0.0081-0.34680.04870.10760.02360.03790.07180.00680.07689.41042.54465.9268
176.9954-1.412-0.71560.37750.0710.1425-0.44610.56210.1175-0.0318-0.14930.0044-0.347-0.43860.52970.3666-0.048-0.13670.2976-0.03770.2764-2.3001-6.8872-9.1907
185.89372.0560.93943.45821.12811.8916-0.0143-0.71160.34240.2436-0.02250.27160.00360.12970.01360.23130.0478-0.00560.23040.02360.09583.3642-1.229431.8378
198.11625.20851.49455.9161.93541.97090.2583-0.32830.03040.369-0.11660.1012-0.0858-0.2493-0.1010.16120.02460.0420.15910.02570.1103-5.49040.610327.0134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 364 through 395 )B364 - 395
2X-RAY DIFFRACTION2chain 'B' and (resid 396 through 420 )B396 - 420
3X-RAY DIFFRACTION3chain 'B' and (resid 421 through 437 )B421 - 437
4X-RAY DIFFRACTION4chain 'B' and (resid 438 through 496 )B438 - 496
5X-RAY DIFFRACTION5chain 'B' and (resid 497 through 530 )B497 - 530
6X-RAY DIFFRACTION6chain 'B' and (resid 531 through 547 )B531 - 547
7X-RAY DIFFRACTION7chain 'C' and (resid 688 through 694 )C688 - 694
8X-RAY DIFFRACTION8chain 'D' and (resid 687 through 696 )D687 - 696
9X-RAY DIFFRACTION9chain 'A' and (resid 308 through 338 )A308 - 338
10X-RAY DIFFRACTION10chain 'A' and (resid 339 through 363 )A339 - 363
11X-RAY DIFFRACTION11chain 'A' and (resid 364 through 395 )A364 - 395
12X-RAY DIFFRACTION12chain 'A' and (resid 396 through 421 )A396 - 421
13X-RAY DIFFRACTION13chain 'A' and (resid 422 through 438 )A422 - 438
14X-RAY DIFFRACTION14chain 'A' and (resid 439 through 469 )A439 - 469
15X-RAY DIFFRACTION15chain 'A' and (resid 470 through 496 )A470 - 496
16X-RAY DIFFRACTION16chain 'A' and (resid 497 through 531 )A497 - 531
17X-RAY DIFFRACTION17chain 'A' and (resid 532 through 547 )A532 - 547
18X-RAY DIFFRACTION18chain 'B' and (resid 307 through 338 )B307 - 338
19X-RAY DIFFRACTION19chain 'B' and (resid 339 through 363 )B339 - 363

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