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- PDB-3hm1: Crystal structure of human Estrogen Receptor Alpha Ligand-Binding... -

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Basic information

Entry
Database: PDB / ID: 3hm1
TitleCrystal structure of human Estrogen Receptor Alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II Peptide and estrone ((8R,9S,13S,14S)-3-hydroxy-13-methyl-7,8,9,11,12,14,15,16-octahydro-6H-cyclopenta[a]phenanthren-17-one)
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / estrogen receptor / LBD / GRIP peptide / estrone / Alternative splicing / DNA-binding / Glycoprotein / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Steroid-binding / Transcription regulation / Zinc / Zinc-finger / Activator / HORMONE / NUCLEAR RECEPTOR
Function / homology
Function and homology information


HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / Regulation of lipid metabolism by PPARalpha / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 ...HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / Regulation of lipid metabolism by PPARalpha / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway / nuclear glucocorticoid receptor binding / nuclear retinoic acid receptor binding / positive regulation of female receptivity / nuclear thyroid hormone receptor binding / 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 / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / 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 / protein localization to chromatin / DNA polymerase binding / steroid binding / 14-3-3 protein binding / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of DNA-binding transcription factor activity / negative regulation of miRNA transcription / response to progesterone / nitric-oxide synthase regulator activity / ESR-mediated signaling / TBP-class protein binding / cerebellum development / 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 / circadian regulation of gene expression / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / response to estrogen / Regulation of RUNX2 expression and activity / transcription coactivator binding / circadian rhythm / 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 / regulation of gene expression / 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 / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex
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
Chem-J3Z / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsRajan, S.S. / Kim, Y. / Vanek, K. / Liwanag, M. / Joachimiak, A. / Greene, G.L.
CitationJournal: To be Published
Title: Crystal structure of human Estrogen Receptor Alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II Peptide and estrone ((8R,9S,13S,14S)-3- ...Title: Crystal structure of human Estrogen Receptor Alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II Peptide and estrone ((8R,9S,13S,14S)-3-hydroxy-13-methyl-7,8,9,11,12,14,15, 16-octahydro-6H-cyclopenta[a]phenanthren-17-one)
Authors: Rajan, S.S. / Kim, Y. / Vanek, K. / Joachimiak, A. / Greene, G.L.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0436
Polymers61,5034
Non-polymers5412
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-30 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.267, 82.666, 58.989
Angle α, β, γ (deg.)90.00, 109.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29171.514 Da / Num. of mol.: 2 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Transcriptional intermediary factor 2


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: Q9WUI9
#3: Chemical ChemComp-J3Z / (9beta,13alpha)-3-hydroxyestra-1,3,5(10)-trien-17-one / Estrone


Mass: 270.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.15 M potassium bromide 30 %w/v polyethylene glycol MME 2000 , pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2009
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. all: 19088 / Num. obs: 18967 / % possible obs: 86.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.33→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4.9 / Num. unique all: 200 / % possible all: 45.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
XFITdata reduction
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 2G50

2g50


Resolution: 2.33→33.368 Å / SU ML: 0.39 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2889 966 5.12 %
Rwork0.2307 --
obs0.2337 18884 86.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.61 Å2 / ksol: 0.311 e/Å3
Refinement stepCycle: LAST / Resolution: 2.33→33.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3979 0 40 10 4029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.091
X-RAY DIFFRACTIONf_bond_d0.006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.33-2.4510.359850.24931572165753
2.451-2.60450.31471170.27112707282491
2.6045-2.80550.34281460.3182792293893
2.8055-3.08760.32881630.243129323095100
3.0876-3.5340.33761490.24732769291893
3.534-4.45080.25391480.19972412256082
4.4508-33.37110.24611580.19772734289290
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)
13.25530.17160.19362.54240.14014.60560.01840.3588-0.0674-0.2159-0.0560.10960.0633-0.2469-0.00020.3975-0.00060.03750.36260.00020.34714.10530.1688-1.0511
24.3839-0.1419-0.2161.45190.00362.6430.0188-0.28710.01920.0446-0.00250.094-0.11260.005500.37380.0162-0.0030.39290.04030.33765.9991-0.69922.8697
30.00910.01040.02850.0048-0.00090.00610.03070.1869-0.4125-0.30370.08460.27720.1377-0.2072-0.00041.5393-0.18640.05010.6381-0.2341.08189.6964-18.0468-10.7312
40.33850.1622-0.33460.1316-0.24550.32970.1964-0.37490.9338-0.13010.22520.5649-0.7199-0.43930.00761.0305-0.01510.06880.5757-0.32211.0592-3.272415.870927.9757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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