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

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Basic information

Entry
Database: PDB / ID: 5dxb
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P1 and Estradiol
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 2
KeywordsHormone receptor/peptide / Estrogen Receptor Alpha / Somatic Mutataion / Stapled Peptide / Peptide Mimetic / Hormone Receptor / Breast Cancer / Hormone receptor-peptide complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / steroid hormone receptor signaling pathway / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / regulation of toll-like receptor signaling pathway / prostate epithelial cord elongation ...regulation of epithelial cell apoptotic process / steroid hormone receptor signaling pathway / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / regulation of toll-like receptor signaling pathway / prostate epithelial cord elongation / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell development / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / negative regulation of smooth muscle cell apoptotic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / nuclear receptor-mediated steroid hormone signaling pathway / mammary gland alveolus development / cellular response to estrogen stimulus / : / 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 / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / cellular response to hormone stimulus / estrogen receptor signaling pathway / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein localization to chromatin / peroxisome proliferator activated receptor signaling pathway / response to progesterone / 14-3-3 protein binding / regulation of cellular response to insulin stimulus / positive regulation of adipose tissue development / BMAL1:CLOCK,NPAS2 activates circadian expression / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / stem cell differentiation / transcription corepressor binding / transcription coregulator binding / negative regulation of canonical NF-kappaB signal transduction / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / 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 / beta-catenin binding / mRNA transcription by RNA polymerase II / response to estrogen / male gonad development / nuclear receptor activity / transcription coactivator binding / positive regulation of fibroblast proliferation / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / 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 / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation
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: 2.08 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/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM104601 United States
National Institutes of Health/Office of the DirectorT32-AT007533 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH) 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 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization ..._pdbx_audit_support.country / _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 / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
D: Nuclear receptor coactivator 2
E: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2189
Polymers62,4544
Non-polymers7645
Water2,936163
1
B: Estrogen receptor
E: Nuclear receptor coactivator 2
hetero molecules

A: Estrogen receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2189
Polymers62,4544
Non-polymers7645
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5280 Å2
ΔGint-36 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.013, 85.939, 58.272
Angle α, β, γ (deg.)90.00, 108.41, 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: 29820.213 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: 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

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Protein/peptide , 1 types, 2 molecules DE

#3: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


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 , 4 types, 168 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / 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: 2.077→27.59 Å / Num. obs: 29401 / % possible obs: 98.3 % / Redundancy: 3.7 % / Net I/σ(I): 2.17
Reflection shellResolution: 2.077→2.1438 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.22 / % possible all: 64

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementResolution: 2.08→27.59 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1502 5.11 %
Rwork0.177 --
obs0.179 29399 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 53 163 3996
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073959
X-RAY DIFFRACTIONf_angle_d1.4345358
X-RAY DIFFRACTIONf_dihedral_angle_d15.5221528
X-RAY DIFFRACTIONf_chiral_restr0.072629
X-RAY DIFFRACTIONf_plane_restr0.005661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0768-2.14380.26021000.22121719X-RAY DIFFRACTION64
2.1438-2.22040.23891060.20192131X-RAY DIFFRACTION78
2.2204-2.30930.21791150.20742483X-RAY DIFFRACTION91
2.3093-2.41430.24981380.2052658X-RAY DIFFRACTION98
2.4143-2.54150.2551330.19912714X-RAY DIFFRACTION99
2.5415-2.70060.23591540.20272668X-RAY DIFFRACTION99
2.7006-2.90890.23041570.19622692X-RAY DIFFRACTION99
2.9089-3.20130.24011460.18852708X-RAY DIFFRACTION99
3.2013-3.66360.21341570.16892696X-RAY DIFFRACTION99
3.6636-4.61230.17011550.14252712X-RAY DIFFRACTION99
4.6123-27.59590.17251410.16012716X-RAY DIFFRACTION97
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)
12.53740.0068-0.39141.27380.03820.99440.01150.05970.0319-0.0342-0.0127-0.0299-0.0453-0.040.0020.1503-0.00740.00720.1571-0.00940.099715.8361-1.22295.1421
22.2708-0.37991.08881.759-0.55263.9182-0.0351-0.1056-0.09220.2190.0048-0.0568-0.00430.23560.0240.2143-0.00660.04940.1913-0.01920.15526.735-1.179429.6363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ -10:9999)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ -10:9999)

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