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- PDB-2b23: Human estrogen receptor alpha ligand-binding domain and a glucoco... -

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Basic information

Entry
Database: PDB / ID: 2b23
TitleHuman estrogen receptor alpha ligand-binding domain and a glucocorticoid receptor-interacting protein 1 NR box II peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / ESTROGEN RECEPTOR / LBD / GRIP PEPTIDE / HORMONE-GROWTH FACTOR RECEPTOR 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity ...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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / 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 / androgen metabolic process / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / 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 / 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 / Zinc finger, C4 type (two domains) / 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
Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRajan, S.S. / Hsieh, R.W. / Sharma, S.K. / Greene, G.L.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: NFkappaB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses
Authors: Nettles, K.W. / Bruning, J.B. / Gil, G. / Nowak, J. / Sharma, S.K. / Hahm, J.B. / Kulp, K. / Hochberg, R.B. / Zhou, H. / Katzenellenbogen, J.A. / Katzenellenbogen, B.S. / Kim, Y. / Joachmiak, A. / Greene, G.L.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.8Oct 16, 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


Theoretical massNumber of molelcules
Total (without water)62,2164
Polymers62,2164
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.372, 80.905, 58.241
Angle α, β, γ (deg.)90.00, 109.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERHISHISAA305 - 5478 - 250
21SERSERHISHISBB305 - 5478 - 250
12LYSLYSASPASPCC688 - 6963 - 11
22LYSLYSASPASPDD688 - 6963 - 11

NCS ensembles :
ID
1
2

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Components

#1: Protein Estrogen receptor / ER / Estradiol receptor / ER-alpha


Mass: 29527.887 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN / Mutation: S537Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: MCSG7 (PET12-DERIVATIVE) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / Fragment: RESIDUES 686 - 698 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. / References: UniProt: Q15596
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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 Å3/Da / Density % sol: 39.4 %
Crystal growpH: 4.5 / Details: pH 4.50

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 30529 / % possible obs: 94.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.965
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.318 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALEPACKdata scaling
XTALVIEWrefinement
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZKY

1zky


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 13.002 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27211 1338 5.1 %RANDOM
Rwork0.21414 ---
obs0.2172 24941 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.637 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.51 Å2
2--0.8 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 0 30 3902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213978
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9835360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75924.012172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91915751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3021522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022834
X-RAY DIFFRACTIONr_nbd_refined0.2350.31956
X-RAY DIFFRACTIONr_nbtor_refined0.3150.52737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.5228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3940.52
X-RAY DIFFRACTIONr_mcbond_it2.391.52481
X-RAY DIFFRACTIONr_mcangle_it3.4623868
X-RAY DIFFRACTIONr_scbond_it5.33531668
X-RAY DIFFRACTIONr_scangle_it7.1854.51492
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1810medium positional0.60.5
2C79medium positional0.820.5
1A1810medium thermal2.622
2C79medium thermal2.412
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 108 -
Rwork0.223 1927 -
obs--99.17 %
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)
11.75480.1864-0.35880.5943-0.01170.4481-0.07980.1048-0.1293-0.01-0.0108-0.05640.02260.02610.0906-0.0399-0.00120.0047-0.0375-0.0038-0.0346-15.7282-0.31544.1053
20.3531-0.18130.31710.4379-0.0981.9513-0.0526-0.13740.00070.07830.00620.0099-0.0244-0.00120.0463-0.0273-0.01190.0109-0.0214-0.0168-0.0469-23.92090.812728.1731
37.6251-0.315-0.588513.2772-0.66844.6686-0.03870.19620.566-0.3436-0.2346-0.9456-0.15910.38590.2733-0.1131-0.0020.1045-0.06380.05790.1185-0.397713.26731.8484
432.92047.93260.57446.82525.33368.44290.22-0.9499-1.50620.51440.08740.0001-0.0241-0.2457-0.30740.0154-0.05730.0223-0.00910.2063-0.0126-24.8942-18.105835.7265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA305 - 5488 - 251
2X-RAY DIFFRACTION2BB305 - 5478 - 250
3X-RAY DIFFRACTION3CC687 - 6962 - 11
4X-RAY DIFFRACTION4DD688 - 6963 - 11

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