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

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Basic information

Entry
Database: PDB / ID: 5dxg
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled Peptide SRC2-P5
Components
  • Estrogen receptor
  • Stapled Peptide SRC2-P5
KeywordsHormone Receptor/peptide / Estrogen Receptor / Hormone / Stapled Peptide / Peptide Mimetic / Breast Cancer / Hormone Receptor-peptide complex
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / 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 / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...regulation of epithelial cell apoptotic process / 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 / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / 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 receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / RNA polymerase II preinitiation complex assembly / positive regulation of DNA-binding transcription factor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / positive regulation of adipose tissue development / protein localization to chromatin / : / steroid binding / Regulation of lipid metabolism by PPARalpha / 14-3-3 protein binding / peroxisome proliferator activated receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / negative regulation of DNA-binding transcription factor activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / response to progesterone / nitric-oxide synthase regulator activity / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / TBP-class protein binding / transcription coregulator binding / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / negative regulation of smoothened signaling pathway / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / euchromatin / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / Regulation of RUNX2 expression and activity / transcription coactivator binding / nuclear receptor activity / Ovarian tumor domain proteases / : / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of inflammatory response
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, DUF1518 ...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, 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: 1.86 Å
AuthorsFanning, S.W. / Speltz, T.E. / Mayne, C.G. / Tajkhorshid, E. / Greene, G.L. / Moore, T.W.
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 1.1Feb 19, 2020Group: Data collection / Derived calculations
Category: pdbx_prerelease_seq / pdbx_struct_assembly ...pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 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
C: Stapled Peptide SRC2-P5
D: Stapled Peptide SRC2-P5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4338
Polymers62,7044
Non-polymers7294
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-25 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.121, 85.274, 58.613
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 Stapled Peptide SRC2-P5


Mass: 1439.728 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3,350, 200 mM MgCl2, 100 mM Tris pH 8.0

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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: 1.856→31.44 Å / Num. obs: 43585 / % possible obs: 99.9 % / Redundancy: 3.7 % / Net I/σ(I): 1.7
Reflection shellResolution: 1.86→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.7 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 1.86→31.44 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 2211 5.07 %
Rwork0.167 --
obs0.169 32596 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→31.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 52 382 4202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084005
X-RAY DIFFRACTIONf_angle_d1.3985416
X-RAY DIFFRACTIONf_dihedral_angle_d14.3541547
X-RAY DIFFRACTIONf_chiral_restr0.049630
X-RAY DIFFRACTIONf_plane_restr0.005669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8555-1.89590.27121220.24022208X-RAY DIFFRACTION85
1.8959-1.940.31551460.21982471X-RAY DIFFRACTION95
1.94-1.98850.22491360.21112578X-RAY DIFFRACTION99
1.9885-2.04220.20771330.19552632X-RAY DIFFRACTION100
2.0422-2.10230.24281230.18332621X-RAY DIFFRACTION100
2.1023-2.17020.22491540.17122630X-RAY DIFFRACTION100
2.1702-2.24770.20881580.17092597X-RAY DIFFRACTION100
2.2477-2.33770.20681250.16882615X-RAY DIFFRACTION100
2.3377-2.4440.2041450.16822625X-RAY DIFFRACTION100
2.444-2.57280.21921580.17052583X-RAY DIFFRACTION100
2.5728-2.73390.19021230.17242627X-RAY DIFFRACTION100
2.7339-2.94490.21081440.16992647X-RAY DIFFRACTION100
2.9449-3.2410.20231370.16272618X-RAY DIFFRACTION100
3.241-3.70930.16961320.15072656X-RAY DIFFRACTION100
3.7093-4.67090.15361490.13442618X-RAY DIFFRACTION99
4.6709-31.44730.20151260.16752645X-RAY DIFFRACTION98
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)
16.7749-3.19820.6673.7205-1.13631.44670.04610.49760.398-0.1747-0.0601-0.172-0.0614-0.18290.00420.1513-0.0323-0.01980.1618-0.02830.078416.4171.5609-4.2377
21.6444-0.4233-0.34872.46230.07130.8497-0.01970.0788-0.1462-0.0717-0.00040.08330.07560.00910.00960.0977-0.0131-0.00120.1016-0.01330.07520.0869-0.34694.7074
33.8719-0.4768-0.05060.75050.03740.7557-0.01160.11150.20030.0117-0.0037-0.0303-0.0583-0.05240.02030.1054-0.0010.00130.08430.00030.090611.04314.60019.303
43.7933-0.34211.92462.0186-0.0143.8426-0.1099-0.5513-0.17960.26180.06120.32280.1018-0.63270.08070.2480.05980.07960.27540.0640.1602-3.86821.003534.8743
52.2894-0.3850.33082.9815-0.22933.4767-0.1227-0.15320.02570.28080.0226-0.0697-0.21630.19090.06820.2110.00250.00010.1307-0.00510.097210.04725.957832.8727
64.04320.4241.61651.9926-1.05233.6763-0.0747-0.0498-0.1830.0318-0.0050.05560.0934-0.13810.08640.0859-0.00960.040.1158-0.01330.1035-4.19030.454721.8441
74.7376-0.75442.73391.8357-0.74963.9886-0.0885-0.1913-0.03940.19640.0311-0.2113-0.01570.35040.08080.14810.00260.03110.1832-0.01460.115613.023.067325.7518
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 338 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 339 THROUGH 437 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 438 THROUGH 496 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 497 THROUGH 548 )

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