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- PDB-6pit: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

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Basic information

Entry
Database: PDB / ID: 6pit
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with SRC2 Stapled Peptide 41A and Estradiol
Components
  • (Estrogen receptor) x 2
  • Stapled Peptide 41A
KeywordsTRANSCRIPTION / Hormone / Nuclear Receptor / Estrogen / Stapled Peptide
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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / 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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / calmodulin binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / 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 / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsFanning, S.W. / Montgomery, J.E. / Greene, G.L. / Moellering, R.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Versatile Peptide Macrocyclization with Diels-Alder Cycloadditions.
Authors: Montgomery, J.E. / Donnelly, J.A. / Fanning, S.W. / Speltz, T.E. / Shangguan, X. / Coukos, J.S. / Greene, G.L. / Moellering, R.E.
History
DepositionJun 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 4, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.3Oct 11, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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
D: Stapled Peptide 41A
C: Stapled Peptide 41A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6176
Polymers63,0724
Non-polymers5452
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-23 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.534, 71.030, 58.082
Angle α, β, γ (deg.)90.000, 108.680, 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: 29949.326 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: 29949.326 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
#3: Protein/peptide Stapled Peptide 41A


Mass: 1586.770 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-EST / ESTRADIOL


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


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 20 mM Tris pH 8.0, 15% PEG 3,350, 200 mM 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: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 18168 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rpim(I) all: 0.136 / Net I/σ(I): 13.5
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 2.4 % / Num. unique obs: 6634 / CC1/2: 0.51 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIXv1.9refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CBZ

6cbz


Resolution: 2.25→43.5 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.247 --
Rwork0.214 --
obs-6634 99.5 %
Displacement parametersBiso max: 97.01 Å2 / Biso mean: 37.2929 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 57 152 3696
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)
17.2665-3.02243.6855.0335-1.09614.12080.16030.47820.0312-0.6846-0.11510.01670.18720.3433-0.01310.3129-0.01940.050.25050.00440.132216.6976-2.7194-7.67
22.69360.13050.33198.2360.56462.31610.1677-0.0502-0.0934-0.2296-0.17470.0970.09710.03150.02440.1556-0.0078-0.00580.2060.00660.12113.0295-0.9518-2.424
33.3984-0.92331.49373.24190.73652.4401-0.0002-0.23220.2035-0.0506-0.06580.3303-0.2272-0.11590.10150.18170.01750.02480.25130.01540.230113.4445.35573.3013
42.98151.15170.63559.23741.71672.38540.1488-0.2416-0.48810.32410.0399-0.22730.3780.1922-0.13890.25240.0816-0.05710.37410.05010.277926.5643-8.05479.8952
56.8531-0.09936.53542.33010.48816.9884-0.2056-0.5359-0.09190.0180.12020.0341-0.3303-0.45490.03920.19630.02120.05710.23850.01590.131212.3143.19888.9222
69.1452-3.56881.83849.49221.03378.37060.40630.6847-1.8772-0.90080.23551.07730.8345-0.1409-0.67170.4178-0.1209-0.14150.374-0.01440.6062-0.3846-7.3965-6.1039
76.4391-2.2597-1.96629.9153-2.87038.2412-0.1276-0.96311.29931.0636-0.0662-1.1294-0.57910.33830.34440.4214-0.0397-0.10370.6197-0.12010.409319.74177.276734.2019
85.27880.2265-0.64965.4094-0.15213.82120.108-0.4848-0.02540.3513-0.1567-0.0286-0.22330.02440.05850.18590.0111-0.00270.2579-0.00030.13821.71010.547227.815
91.9881-0.29653.87912.0182-0.08371.1802-0.20980.3997-2.3167-0.79270.33270.04111.1666-0.5069-0.21220.4821-0.21150.08180.4016-0.00430.6345-6.0146-16.303821.4502
105.8781.169-0.13636.58891.58742.1104-0.11320.1851-0.2625-0.075-0.0162-0.12610.09440.08690.1030.17980.00780.04640.31820.01160.11410.6676-4.68921.6265
114.3734-0.4675-1.68168.49480.7543.4072-0.1452-0.27910.86210.44710.0459-0.4734-0.32790.4240.11970.2013-0.0638-0.06010.3833-0.02240.341523.62834.500624.6933
128.96170.21761.24151.34780.33530.7209-0.12820.69550.4344-0.1321-0.00760.2411-0.0823-0.0460.09260.2417-0.0128-0.0130.31960.06790.18382.6837-1.152816.8351
136.78391.06730.22970.65871.62595.1795-0.77090.78450.0498-0.8642-0.3288-0.47561.22910.69850.99711.33190.1921-0.01080.72090.10570.861312.5879-16.9661-9.0743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 307:363 )A307 - 363
2X-RAY DIFFRACTION2(CHAIN A AND RESID 364:411 )A364 - 411
3X-RAY DIFFRACTION3(CHAIN A AND RESID 412:465 )A412 - 465
4X-RAY DIFFRACTION4(CHAIN A AND RESID 466:496 )A466 - 496
5X-RAY DIFFRACTION5(CHAIN A AND RESID 497:528 )A497 - 528
6X-RAY DIFFRACTION6(CHAIN A AND RESID 529:547 )A529 - 547
7X-RAY DIFFRACTION7(CHAIN B AND RESID 308:321 )B308 - 321
8X-RAY DIFFRACTION8(CHAIN B AND RESID 322:407 )B322 - 407
9X-RAY DIFFRACTION9(CHAIN B AND RESID 408:421 )B408 - 421
10X-RAY DIFFRACTION10(CHAIN B AND RESID 422:473 )B422 - 473
11X-RAY DIFFRACTION11(CHAIN B AND RESID 474:496 )B474 - 496
12X-RAY DIFFRACTION12(CHAIN B AND RESID 497:547 )B497 - 547
13X-RAY DIFFRACTION13(CHAIN C AND RESID 7:9 )C7 - 9

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