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- PDB-3l03: Crystal Structure of human Estrogen Receptor alpha Ligand-Binding... -

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Basic information

Entry
Database: PDB / ID: 3l03
TitleCrystal Structure of human Estrogen Receptor alpha Ligand-Binding Domain in complex with a Glucocorticoid Receptor Interacting Protein 1 Nr Box II peptide and Estetrol (Estra-1,3,5(10)-triene-3,15 alpha,16alpha,17beta-tetrol)
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / estrogen receptor / LBD / GRIP peptide / estetrol / DNA-binding / Glycoprotein / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Receptor / Steroid-binding / Transcription regulation / Zinc-finger / Activator
Function / homology
Function and homology information


HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Endogenous sterols / Synthesis of bile acids and bile salts / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Regulation of lipid metabolism by PPARalpha / cellular response to Thyroglobulin triiodothyronine ...HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Endogenous sterols / Synthesis of bile acids and bile salts / Recycling of bile acids and salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Regulation of lipid metabolism by PPARalpha / cellular response to Thyroglobulin triiodothyronine / 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 / steroid hormone receptor signaling pathway / 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 / nuclear estrogen receptor activity / locomotor rhythm / Developmental Lineage of Mammary Gland Alveolar Cells / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of glucose metabolic process / negative regulation of smooth muscle cell apoptotic process / Synthesis of bile acids and bile salts / response to progesterone / nuclear receptor-mediated steroid hormone signaling pathway / cellular response to estrogen stimulus / Developmental Lineage of Mammary Gland Luminal Epithelial Cells / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / cerebellum development / regulation of lipid metabolic process / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / nuclear retinoid X receptor binding / Nuclear signaling by ERBB4 / Recycling of bile acids and salts / transcription regulator inhibitor activity / estrogen receptor signaling pathway / RNA polymerase II preinitiation complex assembly / cellular response to hormone stimulus / steroid binding / positive regulation of nitric-oxide synthase activity / peroxisome proliferator activated receptor signaling pathway / Regulation of lipid metabolism by PPARalpha / stem cell differentiation / positive regulation of adipose tissue development / protein localization to chromatin / bile acid and bile salt transport / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / DNA polymerase binding / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / 14-3-3 protein binding / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / male gonad development / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear receptor binding / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / negative regulation of canonical NF-kappaB signal transduction / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / circadian regulation of gene expression / Heme signaling / circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / euchromatin / Nuclear Receptor transcription pathway / negative regulation of smoothened signaling pathway / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / response to estrogen / mRNA transcription by RNA polymerase II / beta-catenin binding / nuclear receptor activity / regulation of gene expression / positive regulation of nitric oxide biosynthetic process / transcription coregulator activity / Constitutive Signaling by Aberrant PI3K in Cancer / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / transcription coactivator binding / phospholipase C-activating G protein-coupled receptor signaling pathway / Regulation of RUNX2 expression and activity / response to estradiol
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
Chem-4OH / Estrogen receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsRajan, S.S. / Kim, Y. / Vanek, K. / 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 Estra-1,3,5(10)-triene-3,15 ...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 Estra-1,3,5(10)-triene-3,15 alpha,16alpha,17beta-tetrol
Authors: Rajan, S.S. / Kim, Y. / Vanek, K. / Joachimiak, A. / Greene, G.L.
History
DepositionDec 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity_name_com.name ..._entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)61,9358
Polymers61,1984
Non-polymers7364
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-37 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.027, 84.203, 58.762
Angle α, β, γ (deg.)90.00, 109.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 29019.279 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 / Plasmid: MCSG7 (pET12-derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596, UniProt: Q9WUI9*PLUS

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Non-polymers , 4 types, 136 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-4OH / (14beta,15alpha,16alpha,17alpha)-estra-1,3,5(10)-triene-3,15,16,17-tetrol / Estra-1,3,5(10)-triene-3,15 alpha,16alpha,17beta-tetrol


Mass: 304.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O4 / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSOME OF THE CYS RESIDUES WERE OXIDIZED TO CME. THE AUTHORS WERE ONLY ABLE TO DETECT CME AT POSITION ...SOME OF THE CYS RESIDUES WERE OXIDIZED TO CME. THE AUTHORS WERE ONLY ABLE TO DETECT CME AT POSITION 530 FROM THE ELECTRON DENSITY MAP.

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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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15% (v/v) ethanol, HEPES pH 7.5, MgCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2009 / Details: mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.896→50 Å / Num. all: 40926 / Num. obs: 40149 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 29.52 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 39.365
Reflection shellResolution: 1.896→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 1636

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Processing

Software
NameVersionClassification
HKL-3000data collection
Auto-Rickshawphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDb entry 1ZKY

1zky


Resolution: 1.896→32.954 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1882 5 %RANDOM
Rwork0.1757 ---
obs0.1781 40081 91.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.702 Å2 / ksol: 0.382 e/Å3
Refinement stepCycle: LAST / Resolution: 1.896→32.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 51 132 4180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134166
X-RAY DIFFRACTIONf_angle_d1.4385641
X-RAY DIFFRACTIONf_dihedral_angle_d18.1631585
X-RAY DIFFRACTIONf_chiral_restr0.089672
X-RAY DIFFRACTIONf_plane_restr0.006692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.896-1.96340.31811240.25512632275667
1.9634-2.0420.31811690.21493251342084
2.042-2.13490.25591700.20313499366990
2.1349-2.24750.27361680.19143660382893
2.2475-2.38820.26321630.18193662382594
2.3882-2.57260.24591870.18543753394096
2.5726-2.83130.25832240.19953738396297
2.8313-3.24070.21312110.18863840405199
3.2407-4.08180.18832220.151138704092100
4.0818-32.95880.18332440.15183857410198
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.73580.43860.23711.06650.39641.665-0.08590.0644-0.0681-0.18870.0632-0.0178-0.0610.0089-00.2413-0.0135-0.00510.2110.00730.2209-33.981916.44327.1212
21.3330.1726-1.0010.940.01271.26850.1177-0.1310.06150.0398-0.0380.0863-0.08240.0424-00.1904-0.0165-0.00080.1864-0.01060.1772
30.0292-0.00080.0180.00610.00740.0118-0.04860.0624-0.1878-0.1365-0.1117-0.16650.20090.10170.00060.505-0.13930.01490.4666-0.12620.3284
40.0041-0.0031-0.00050.0078-0.0002-0.00010.0638-0.19420.17770.1227-0.05710.0557-0.2022-0.0464-0.00020.4614-0.04350.19160.3861-0.18290.6363
Refinement TLS groupSelection details: chain D

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