[English] 日本語
Yorodumi
- PDB-7xvy: Human Estrogen Receptor beta Ligand-binding Domain in Complex wit... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity / male mating behavior / hypothalamus development / nuclear steroid receptor activity ...receptor antagonist activity / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity / male mating behavior / hypothalamus development / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / estrous cycle / nuclear retinoid X receptor binding / positive regulation of DNA-binding transcription factor activity / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / lactation / : / steroid binding / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / ESR-mediated signaling / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / negative regulation of cell growth / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / : / response to estradiol / cell-cell signaling / PIP3 activates AKT signaling / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / Extra-nuclear estrogen signaling / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / 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 / 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
(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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more