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- PDB-5wgq: Estrogen Receptor Alpha Ligand Binding Domain in Complex with Est... -

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Basic information

Entry
Database: PDB / ID: 5wgq
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with Estradiol and SRC2-BCP1
Components
  • Estrogen receptor
  • SRC2-BCP1
Keywordstranscription/transcription inhibitor / Breast Cancer / Stapled Peptides / Synthetic Peptides / Hormone. / TRANSCRIPTION / transcription-transcription inhibitor complex
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / transcription regulator inhibitor activity / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / positive regulation of adipose tissue development / steroid binding / : / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of DNA-binding transcription factor activity / nitric-oxide synthase regulator activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / ESR-mediated signaling / TBP-class protein binding / Activation of gene expression by SREBF (SREBP) / response to progesterone / negative regulation of DNA-binding transcription factor activity / transcription coregulator binding / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / transcription coactivator binding / euchromatin / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / male gonad development / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / : / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific
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
SRC2-BCP1 / ESTRADIOL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFanning, S.W. / Speltz, T.E. / Mayne, C.G. / Siddiqui, Z. / Greene, G.L. / Tajkhorshid, E. / Moore, T.W.
CitationJournal: Org. Biomol. Chem. / Year: 2018
Title: A "cross-stitched" peptide with improved helicity and proteolytic stability.
Authors: Speltz, T.E. / Mayne, C.G. / Fanning, S.W. / Siddiqui, Z. / Tajkhorshid, E. / Greene, G.L. / Moore, T.W.
History
DepositionJul 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Structure summary / Category: pdbx_molecule / pdbx_molecule_features
Item: _pdbx_molecule.prd_id / _pdbx_molecule_features.prd_id
Revision 1.2Feb 26, 2020Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Revision 1.3Oct 4, 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 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
E: SRC2-BCP1
F: SRC2-BCP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8686
Polymers62,3244
Non-polymers5452
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-27 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.038, 84.044, 58.209
Angle α, β, γ (deg.)90.00, 111.25, 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: 29774.123 Da / Num. of mol.: 2 / Mutation: Y364S
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 SRC2-BCP1


Type: Oligopeptide / Class: Inhibitor / Mass: 1387.692 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: SRC2-BCP1, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3,350, Tris pH 8.5, MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.295→50 Å / Num. obs: 21421 / % possible obs: 98.3 % / Redundancy: 3.7 % / Net I/σ(I): 0.18
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.4 % / % possible all: 97.6

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Processing

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

5dxe


Resolution: 2.3→31.08 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 977 4.9 %
Rwork0.199 --
obs0.202 19933 91.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 0 40 106 3866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063890
X-RAY DIFFRACTIONf_angle_d1.7375279
X-RAY DIFFRACTIONf_dihedral_angle_d14.6051481
X-RAY DIFFRACTIONf_chiral_restr0.061632
X-RAY DIFFRACTIONf_plane_restr0.006649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2953-2.41620.3013980.24582115X-RAY DIFFRACTION71
2.4162-2.56750.30761150.24552455X-RAY DIFFRACTION83
2.5675-2.76570.26661250.24352771X-RAY DIFFRACTION94
2.7657-3.04380.27471470.23282915X-RAY DIFFRACTION99
3.0438-3.48370.29351820.21592876X-RAY DIFFRACTION99
3.4837-4.38710.22561650.16492899X-RAY DIFFRACTION98
4.3871-31.08660.23381450.17082925X-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)
12.9286-0.42332.04671.5984-0.0912.506-0.0558-0.35090.05960.1905-0.06020.01050.0192-0.19670.08020.34590.01540.07030.40640.00720.246-17.927815.87938.1127
21.65950.31480.09483.8980.8932.9632-0.0024-0.0398-0.00220.21050.04610.0323-0.1345-0.05-0.03740.19330.0235-0.0020.25060.03130.2074-12.821417.94452.9003
31.55470.39260.19991.1029-0.35450.6622-0.01270.02310.08060.0426-0.00320.0932-0.1068-0.1175-0.00350.2710.0177-0.01180.3777-0.01370.2394-21.458518.7822-7.2975
42.8644-1.9342.04792.0955-1.50012.72570.13280.0007-0.08410.0463-0.10730.08680.10820.0824-0.00050.2145-0.0079-0.00450.39260.00930.2317-9.345615.5646-3.4771
50.9949-0.326-0.15672.6423-0.00110.50440.01950.21690.1956-0.0818-0.0957-0.0482-0.10940.09280.06590.1811-0.00850.00570.27290.00670.1697-2.871619.5427-27.8528
66.0384-0.94331.50352.85940.35871.9716-0.27810.7998-0.87410.05780.17070.2867-0.289-0.05060.12860.2269-0.04360.04660.2363-0.0890.3322-3.06170.6424-26.5163
78.1765-3.48922.62073.4018-0.88643.1429-0.49620.2936-0.61250.09720.29540.24070.08780.05530.25060.3429-0.07370.02220.26350.02460.3396-10.9494.4751-20.4629
83.4018-1.17010.24371.0087-0.21661.0068-0.02810.0070.01480.05050.0204-0.051-0.01430.09230.01520.2634-0.0325-0.02010.32790.00410.2557-10.638719.2435-20.0988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 308:363 )A308 - 363
2X-RAY DIFFRACTION2( CHAIN A AND RESID 364:420 )A364 - 420
3X-RAY DIFFRACTION3( CHAIN A AND RESID 421:496 )A421 - 496
4X-RAY DIFFRACTION4( CHAIN A AND RESID 497:547 )A497 - 547
5X-RAY DIFFRACTION5( CHAIN B AND RESID 306:394 )B306 - 394
6X-RAY DIFFRACTION6( CHAIN B AND RESID 395:421 )B395 - 421
7X-RAY DIFFRACTION7( CHAIN B AND RESID 422:437 )B422 - 437
8X-RAY DIFFRACTION8( CHAIN B AND RESID 438:548 )B438 - 548

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