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- PDB-5dx3: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

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Basic information

Entry
Database: PDB / ID: 5dx3
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P3 and Estradiol
Components
  • (Estrogen receptor) x 2
  • Stapled Peptide SRC2-P3
KeywordsHormone receptor/peptide / Synthetic Peptide / Stapled Peptide / Estrogen Receptor Alpha / Somatic Mutation / Peptide Mimetic / AF-2 Binding / 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 / cellular response to Thyroglobulin triiodothyronine ...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 / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / negative regulation of smooth muscle cell apoptotic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / 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 / Recycling of bile acids and salts / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / estrogen receptor signaling pathway / 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 / response to progesterone / positive regulation of adipose tissue development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein localization to chromatin / 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 miRNA transcription / TBP-class protein binding / stem cell differentiation / 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 / negative regulation of smoothened signaling pathway / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / 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 / 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 / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / 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
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 / Resolution: 2.0903 Å
AuthorsSpeltz, T.E. / Fanning, S.W. / Mayne, C.G. / Tajkhorshid, E. / Greene, G.L. / Moore, T.W.
Funding support United States, 6items
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/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM104601 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)T32 AT007533 United States
National Science Foundation (NSF, United States)MCA06N060 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 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: Stapled Peptide SRC2-P3
D: Stapled Peptide SRC2-P3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0167
Polymers62,4364
Non-polymers5803
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-26 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.162, 85.851, 58.764
Angle α, β, γ (deg.)90.00, 109.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 29774.123 Da / Num. of mol.: 1 / 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 Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29802.174 Da / Num. of mol.: 1 / 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

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Stapled Peptide SRC2-P3


Mass: 1429.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596

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Non-polymers , 3 types, 143 molecules

#4: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% 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: 2.09→26.54 Å / Num. all: 30635 / Num. obs: 29884 / % possible obs: 98.5 % / Redundancy: 3.7 % / Net I/σ(I): 1.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 2.0903→26.536 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1447 4.84 %
Rwork0.2098 --
obs0.212 29873 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0903→26.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3757 0 41 140 3938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093906
X-RAY DIFFRACTIONf_angle_d1.5375293
X-RAY DIFFRACTIONf_dihedral_angle_d16.0071504
X-RAY DIFFRACTIONf_chiral_restr0.064632
X-RAY DIFFRACTIONf_plane_restr0.006650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0903-2.1650.28321200.26072492X-RAY DIFFRACTION84
2.165-2.25170.45911280.39822584X-RAY DIFFRACTION87
2.2517-2.35410.34711650.31292798X-RAY DIFFRACTION95
2.3541-2.47810.25081460.22652923X-RAY DIFFRACTION99
2.4781-2.63320.2811530.22062906X-RAY DIFFRACTION99
2.6332-2.83630.27231510.22172943X-RAY DIFFRACTION99
2.8363-3.12140.24661480.21282958X-RAY DIFFRACTION99
3.1214-3.57210.27111560.20122908X-RAY DIFFRACTION99
3.5721-4.49690.20321360.16872972X-RAY DIFFRACTION99
4.4969-26.53850.21331440.172942X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 48.4109 Å / Origin y: 2.2431 Å / Origin z: 72.5397 Å
111213212223313233
T0.162 Å2-0.0103 Å2-0.0095 Å2-0.1321 Å2-0.0045 Å2--0.1914 Å2
L1.0752 °2-0.0703 °2-0.5118 °2-1.0179 °2-0.1489 °2--1.4053 °2
S-0.0224 Å °-0.0876 Å °-0.0512 Å °0.1439 Å °0.0057 Å °-0.0049 Å °-0.0261 Å °0.007 Å °0.0147 Å °
Refinement TLS groupSelection details: all

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