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- PDB-5dxe: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

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Basic information

Entry
Database: PDB / ID: 5dxe
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P4 and Estradiol
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsHormone receptor/peptide / Estrogen Receptor Alpha / Stapled Peptide / Peptide Mimetic / Breast Cancer / Hormone / Somatic Mutation / Hormone receptor-peptide 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 / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / 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
ESTRADIOL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFanning, S.W. / Speltz, T.E. / Mayne, C.G. / Tajkhorshid, E. / Greene, G.L. / Moore, T.W.
Funding support United States, 7items
OrganizationGrant numberCountry
American Association of Colleges of Pharmacy United States
University of Illinois Cancer Center United States
Chicago Biomedical Consortium United States
National Institutes of Health/Office of the DirectorT32 AT007533 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM10461 United States
National Science Foundation (NSF, United States)MCA06N060 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Stapled Peptides with gamma-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction.
Authors: Speltz, T.E. / Fanning, S.W. / Mayne, C.G. / Fowler, C. / Tajkhorshid, E. / Greene, G.L. / Moore, T.W.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.5Mar 11, 2020Group: Derived calculations / Category: struct_conn / Item: _struct_conn.pdbx_value_order
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)63,2016
Polymers62,6564
Non-polymers5452
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-21 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.009, 85.181, 58.291
Angle α, β, γ (deg.)90.00, 108.64, 90.00
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: 29912.396 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 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1415.706 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3,350, 200 mM MgCl2, 100 mM Tris pH 8.0 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→27.61 Å / Num. obs: 72916 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 1.9
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.2 / % possible all: 20

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DX3

5dx3


Resolution: 1.5→27.61 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 3636 4.99 %
Rwork0.178 --
obs0.179 72914 88.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 40 398 4262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094049
X-RAY DIFFRACTIONf_angle_d1.6285488
X-RAY DIFFRACTIONf_dihedral_angle_d14.6641570
X-RAY DIFFRACTIONf_chiral_restr0.231639
X-RAY DIFFRACTIONf_plane_restr0.006681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5019-1.52170.2838250.2416540X-RAY DIFFRACTION18
1.5217-1.54250.2883420.2392778X-RAY DIFFRACTION26
1.5425-1.56460.2623420.23131143X-RAY DIFFRACTION37
1.5646-1.58790.285840.22451606X-RAY DIFFRACTION54
1.5879-1.61270.28381150.24212254X-RAY DIFFRACTION75
1.6127-1.63920.24891530.2332722X-RAY DIFFRACTION90
1.6392-1.66740.22481520.232954X-RAY DIFFRACTION98
1.6674-1.69770.26551380.22163020X-RAY DIFFRACTION100
1.6977-1.73040.26391520.21472963X-RAY DIFFRACTION100
1.7304-1.76570.22791630.2143023X-RAY DIFFRACTION100
1.7657-1.80410.25051810.21173019X-RAY DIFFRACTION100
1.8041-1.8460.23551710.21612960X-RAY DIFFRACTION100
1.846-1.89220.22111430.20043009X-RAY DIFFRACTION100
1.8922-1.94340.2011540.18993041X-RAY DIFFRACTION100
1.9434-2.00050.20681520.18413033X-RAY DIFFRACTION100
2.0005-2.06510.19691550.17853004X-RAY DIFFRACTION100
2.0651-2.13890.19171670.16952982X-RAY DIFFRACTION100
2.1389-2.22450.2091750.17142999X-RAY DIFFRACTION100
2.2245-2.32560.22921430.1693050X-RAY DIFFRACTION100
2.3256-2.44820.18851580.17523009X-RAY DIFFRACTION100
2.4482-2.60150.18361690.17932981X-RAY DIFFRACTION100
2.6015-2.80210.20711750.18363032X-RAY DIFFRACTION100
2.8021-3.08380.18441510.16943024X-RAY DIFFRACTION100
3.0838-3.52930.17981540.16283054X-RAY DIFFRACTION100
3.5293-4.44350.16321510.13713051X-RAY DIFFRACTION100
4.4435-27.62070.18571710.16973027X-RAY DIFFRACTION99
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)
16.1229-2.94590.57123.4894-1.0291.4553-0.01310.37920.4228-0.13870.0327-0.1625-0.0623-0.2323-0.030.1409-0.0304-0.01320.1477-0.02170.065115.80751.4334-4.3299
21.381-0.1991-0.32612.29520.12630.8048-0.00960.06-0.148-0.0476-0.00260.06210.05010.01650.00440.0658-0.00870.00180.0875-0.01060.065219.6874-0.70374.701
33.5499-0.4221-0.22930.60430.01480.60280.00690.11180.1379-0.0132-0.0019-0.0341-0.032-0.0330.00370.087-0.00230.00490.0758-0.00040.073310.3184.24199.2367
41.8103-0.65810.35682.2451-0.47692.9522-0.1331-0.18490.01580.21130.0788-0.0467-0.20760.0680.03460.18960.00850.01010.1192-0.00620.07587.24544.892933.3093
52.924-0.06660.73291.2637-0.18662.3275-0.0318-0.131-0.09020.08810.0137-0.06370.03680.1430.00680.09240.00690.02010.0894-0.01380.07245.21861.405323.8648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 307 THROUGH 338 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 339 THROUGH 437 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 438 THROUGH 547 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 308 THROUGH 437 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 438 THROUGH 548 )

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