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- PDB-7xvy: Human Estrogen Receptor beta Ligand-binding Domain in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 7xvy
TitleHuman Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN
Components
  • Estrogen receptor beta
  • Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION/INHIBITOR / Inhibitor / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


receptor antagonist activity / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity ...receptor antagonist activity / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / steroid binding / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / cellular response to estradiol stimulus / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / negative regulation of cell growth / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / Circadian Clock / response to estradiol / cell-cell signaling / PIP3 activates AKT signaling / HATs acetylate histones / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 1 / 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 ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 1 / 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 / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / 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
Similarity search - Domain/homology
(2~{S})-2,3-bis(4-hydroxyphenyl)propanenitrile / Nuclear receptor coactivator 1 / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.544 Å
AuthorsFuruya, N. / Handa, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2022
Title: Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
Authors: Handa, C. / Yamazaki, Y. / Yonekubo, S. / Furuya, N. / Momose, T. / Ozawa, T. / Furuishi, T. / Fukuzawa, K. / Yonemochi, E.
History
DepositionMay 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor beta
B: Estrogen receptor beta
C: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6576
Polymers58,1784
Non-polymers4792
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-31 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.194, 89.014, 101.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Estrogen receptor beta / / ER-beta / Nuclear receptor subfamily 3 group A member 2


Mass: 27702.578 Da / Num. of mol.: 2 / Fragment: ligand-binding domain / Mutation: C334S, C369S, C481S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92731
#2: Protein/peptide Nuclear receptor coactivator 1 / / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase
#3: Chemical ChemComp-I0K / (2~{S})-2,3-bis(4-hydroxyphenyl)propanenitrile


Mass: 239.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→46.443 Å / Num. obs: 69739 / % possible obs: 99.6 % / Redundancy: 11.6 % / CC1/2: 0.998 / Net I/σ(I): 18.7
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 511 / CC1/2: 0.577

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Processing

Software
NameVersionClassification
REFMAC5.8.0349refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2giu

2giu


Resolution: 1.544→46.443 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.212 / SU B: 1.563 / SU ML: 0.057 / Average fsc free: 0.9629 / Average fsc work: 0.9724 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 3392 4.869 %RANDOM
Rwork0.2063 66275 --
all0.208 ---
obs-69667 99.514 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.187 Å2-0 Å20 Å2
2--0.17 Å20 Å2
3---0.017 Å2
Refinement stepCycle: LAST / Resolution: 1.544→46.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3543 0 36 320 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123685
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163527
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6144985
X-RAY DIFFRACTIONr_angle_other_deg0.5831.5478199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.6341013
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10810669
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.46410125
X-RAY DIFFRACTIONr_chiral_restr0.0890.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined0.2460.2809
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.23037
X-RAY DIFFRACTIONr_nbtor_refined0.180.21838
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.22012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.214
X-RAY DIFFRACTIONr_nbd_other0.2380.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.213
X-RAY DIFFRACTIONr_mcbond_it2.2252.0391871
X-RAY DIFFRACTIONr_mcbond_other2.2252.0391872
X-RAY DIFFRACTIONr_mcangle_it3.0993.0432337
X-RAY DIFFRACTIONr_mcangle_other3.0993.0442338
X-RAY DIFFRACTIONr_scbond_it3.3512.3831814
X-RAY DIFFRACTIONr_scbond_other3.352.3831815
X-RAY DIFFRACTIONr_scangle_it4.9963.4332647
X-RAY DIFFRACTIONr_scangle_other4.9953.4322648
X-RAY DIFFRACTIONr_lrange_it6.16130.4974270
X-RAY DIFFRACTIONr_lrange_other6.1630.4934271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.544-1.5840.3572140.35746820.35751110.9530.95395.79340.35
1.584-1.6280.3112740.2946760.29149780.9550.96499.43750.276
1.628-1.6750.2662350.2545870.25148230.9610.96899.97930.228
1.675-1.7260.3012100.23745030.23947130.9440.9671000.212
1.726-1.7830.2552060.20443870.20645930.9630.9731000.18
1.783-1.8450.2542120.19641850.19843970.960.9751000.179
1.845-1.9150.2542030.19240790.19442820.9590.9771000.179
1.915-1.9930.2422060.19839000.20141060.9640.9761000.19
1.993-2.0820.2441880.20437780.20639660.9670.9761000.199
2.082-2.1830.2021830.19936110.19937940.9760.9781000.198
2.183-2.3010.2131650.19334380.19436050.9710.97999.94450.194
2.301-2.440.2441750.19432270.19634190.9630.97899.50280.198
2.44-2.6080.2041740.1830470.18232430.9730.9899.32160.19
2.608-2.8160.2151630.19428140.19629910.9690.97699.53190.206
2.816-3.0840.2051400.19226530.19228060.9730.97799.53670.21
3.084-3.4460.2441360.20123990.20425380.9610.97599.88180.226
3.446-3.9750.2061100.17921330.18122440.9730.97999.95540.21
3.975-4.860.214930.17418410.17519340.9760.9811000.208
4.86-6.8350.333720.24414550.24815290.9580.96899.86920.295
6.835-46.4430.304330.3388800.3369150.960.95599.78140.345

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