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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xwr
TitleHuman Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile
Components
  • Estrogen receptor beta
  • SRC peptide
KeywordsTRANSCRIPTION/INHIBITOR / Inhibitor / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


receptor antagonist activity / nuclear estrogen receptor activity / nuclear steroid receptor activity / estrogen response element binding / positive regulation of DNA-binding transcription factor activity / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear estrogen receptor activity / nuclear steroid receptor activity / estrogen response element binding / positive regulation of DNA-binding transcription factor activity / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / Nuclear Receptor transcription pathway / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell signaling / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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-I2B / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.164 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 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Structure summary / Category: citation / struct / Item: _citation.journal_volume / _struct.title
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: SRC peptide
D: SRC peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7266
Polymers58,1784
Non-polymers5472
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-34 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.436, 89.226, 101.532
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 SRC peptide


Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-I2B / (2~{S})-2-(2-chloranyl-4-oxidanyl-phenyl)-3-(4-hydroxyphenyl)propanenitrile


Mass: 273.714 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12ClNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.04 Å3/Da / Density % sol: 39.75 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→46.633 Å / Num. obs: 25917 / % possible obs: 99.3 % / Redundancy: 5.9 % / CC1/2: 0.937 / Rmerge(I) obs: 0.451 / Rpim(I) all: 0.288 / Rrim(I) all: 0.537 / Net I/σ(I): 4.4
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 5.7 % / Rmerge(I) obs: 2.186 / Num. unique obs: 2196 / CC1/2: 0.623 / Rpim(I) all: 1.499 / Rrim(I) all: 2.664

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2giu

2giu


Resolution: 2.164→46.633 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.338 / WRfactor Rwork: 0.264 / SU B: 12.339 / SU ML: 0.294 / Average fsc free: 0.7829 / Average fsc work: 0.8042 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.269
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.3178 1294 5.008 %RANDOM
Rwork0.2614 24546 --
all0.264 ---
obs-25840 98.955 %-
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: 26.142 Å2
Baniso -1Baniso -2Baniso -3
1-3.579 Å2-0 Å20 Å2
2---9.383 Å20 Å2
3---5.804 Å2
Refinement stepCycle: LAST / Resolution: 2.164→46.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3530 0 38 25 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133627
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153532
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6174897
X-RAY DIFFRACTIONr_angle_other_deg1.2891.5728139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88222.941136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10215665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5711514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_nbd_refined0.2220.2876
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.23143
X-RAY DIFFRACTIONr_nbtor_refined0.160.21768
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2930.221
X-RAY DIFFRACTIONr_nbd_other0.2630.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5010.21
X-RAY DIFFRACTIONr_mcbond_it2.2452.7841853
X-RAY DIFFRACTIONr_mcbond_other2.2442.7831852
X-RAY DIFFRACTIONr_mcangle_it3.5814.1552304
X-RAY DIFFRACTIONr_mcangle_other3.5814.1552305
X-RAY DIFFRACTIONr_scbond_it2.4322.9721774
X-RAY DIFFRACTIONr_scbond_other2.4322.9721775
X-RAY DIFFRACTIONr_scangle_it3.9374.3552593
X-RAY DIFFRACTIONr_scangle_other3.9364.3542594
X-RAY DIFFRACTIONr_lrange_it5.79832.5764117
X-RAY DIFFRACTIONr_lrange_other5.79832.5774115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.164-2.220.373910.3761751X-RAY DIFFRACTION98.2924
2.22-2.2810.317930.3431761X-RAY DIFFRACTION98.617
2.281-2.3470.391690.3081701X-RAY DIFFRACTION99.4941
2.347-2.4190.309980.3041645X-RAY DIFFRACTION99.0341
2.419-2.4990.319820.281605X-RAY DIFFRACTION99.0605
2.499-2.5860.292850.2751550X-RAY DIFFRACTION99.3921
2.586-2.6840.326790.2781472X-RAY DIFFRACTION98.6014
2.684-2.7930.304620.2781474X-RAY DIFFRACTION99.0968
2.793-2.9170.321720.2511382X-RAY DIFFRACTION98.7101
2.917-3.060.366600.231337X-RAY DIFFRACTION98.8677
3.06-3.2250.32790.2591251X-RAY DIFFRACTION99.032
3.225-3.420.301680.2381188X-RAY DIFFRACTION99.1318
3.42-3.6560.329750.2271121X-RAY DIFFRACTION98.5985
3.656-3.9490.311700.2291050X-RAY DIFFRACTION99.115
3.949-4.3250.262470.217991X-RAY DIFFRACTION99.3301
4.325-4.8340.3440.198906X-RAY DIFFRACTION99.2685
4.834-5.580.301360.232799X-RAY DIFFRACTION99.1686
5.58-6.8290.434410.269688X-RAY DIFFRACTION99.7264
6.829-9.6360.291290.199547X-RAY DIFFRACTION99.4819
9.636-46.6330.199140.219327X-RAY DIFFRACTION96.6006

+
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