[English] 日本語
Yorodumi
- PDB-1qkn: RAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qkn
TitleRAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH ANTAGONIST RALOXIFENE
ComponentsESTROGEN RECEPTOR BETA
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ANTAGONIST
Function / homology
Function and homology information


negative regulation of behavior / cellular response to magnetism / response to bisphenol A / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / estradiol binding / response to insecticide / epithelial cell maturation involved in prostate gland development / amygdala development ...negative regulation of behavior / cellular response to magnetism / response to bisphenol A / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / estradiol binding / response to insecticide / epithelial cell maturation involved in prostate gland development / amygdala development / response to human chorionic gonadotropin / hormone-mediated apoptotic signaling pathway / Extra-nuclear estrogen signaling / Sertoli cell proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Sertoli cell development / prostate gland development / organic cyclic compound binding / response to genistein / Nuclear Receptor transcription pathway / negative regulation of androgen receptor signaling pathway / steroid hormone binding / hormone binding / response to salt / prostate gland epithelium morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / nuclear steroid receptor activity / hypothalamus development / negative regulation of feeding behavior / heterocyclic compound binding / female gonad development / response to testosterone / nuclear estrogen receptor activity / response to dexamethasone / androgen receptor signaling pathway / uterus development / vagina development / cellular response to organic cyclic compound / estrous cycle / negative regulation of reactive oxygen species metabolic process / behavioral fear response / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / ovarian follicle development / steroid binding / response to nutrient levels / cerebellum development / response to hormone / epithelial cell proliferation / response to activity / cellular response to estradiol stimulus / promoter-specific chromatin binding / protein-DNA complex / negative regulation of smooth muscle cell proliferation / neuron migration / response to organic cyclic compound / brain development / positive regulation of DNA-binding transcription factor activity / response to estrogen / vasodilation / nuclear receptor activity / negative regulation of epithelial cell proliferation / male gonad development / cellular response to xenobiotic stimulus / response to estradiol / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / perikaryon / cellular response to lipopolysaccharide / response to ethanol / cell population proliferation / negative regulation of neuron apoptotic process / sequence-specific DNA binding / learning or memory / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / neuronal cell body / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleus / cytoplasm
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 / Zinc finger, C4 type (two domains) ...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 / 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
ACETATE ION / RALOXIFENE / Estrogen receptor beta
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPike, A.C.W. / Brzozowski, A.M. / Carlquist, M.
Citation
Journal: Embo J. / Year: 1999
Title: Structure of the Ligand-Binding Domain of Oestrogen Receptor Beta in the Presence of a Partial Agonist and a Full Antagonist
Authors: Pike, A.C.W. / Brzozowski, A.M. / Hubbard, R.E. / Bonn, T. / Thorsell, A.-G. / Engstrom, O. / Ljunggren, J. / Gustaffson, J.-A. / Carlquist, M.
#1: Journal: Nature / Year: 1997
Title: Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor
Authors: Brzozowski, A.M. / Pike, A.C.W. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustaffson, J.-A. / Carlquist, M.
History
DepositionJul 27, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2193
Polymers28,6861
Non-polymers5332
Water2,306128
1
A: ESTROGEN RECEPTOR BETA
hetero molecules

A: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4376
Polymers57,3722
Non-polymers1,0654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area3740 Å2
ΔGint-21.4 kcal/mol
Surface area24880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.550, 67.550, 148.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsBIOLOGICAL_UNIT: DIMER

-
Components

#1: Protein ESTROGEN RECEPTOR BETA / OESTROGEN RECEPTOR / ER-LBD


Mass: 28686.002 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH THE ANTAGONIST RALOXIFENE / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Gene: OESTROGEN RECEPTOR BETA / Plasmid: PLEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GI724 / References: UniProt: Q62986
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27NO4S / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBINDS ESTROGENS WITH AN AFFINITY SIMILAR TO THAT OF ERALPHA, AND ACTIVATES EXPRESSION OF REPORTER ...BINDS ESTROGENS WITH AN AFFINITY SIMILAR TO THAT OF ERALPHA, AND ACTIVATES EXPRESSION OF REPORTER GENES CONTAINING ESTROGEN RESPONSE ELEMENTS (ERE) IN AN ESTROGEN-DEPENDENT MANNER.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57 %
Crystal growpH: 4.8
Details: 7.5% (W/V) PEG 4000, 0.1M AMMONIUM ACETATE, 3% (W/V) DIMETHYLFORMAMIDE, 0.025M SODIUM ACETATE, PH 4.8
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of 1:2 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-11 mg/mlprotein1drop
27.5 %(w/v)PEG40001reservoir
30.1 Mammonium acetate1reservoir
43 %(v/v)dimethylformamide1reservoir
525 mMsodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 16904 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.077 / Net I/σ(I): 8.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.467 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 97187 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.467

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERE

1ere


Resolution: 2.25→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24392 / ESU R Free: 0.22001
Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT REFINEMENT. THE C-TERMINAL HELIX (H12) IS VISIBLE BUT POORLY DEFINED IN THE ELECTRON DENSITY MAPS. CONSEQUENTLY THIS ...Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT REFINEMENT. THE C-TERMINAL HELIX (H12) IS VISIBLE BUT POORLY DEFINED IN THE ELECTRON DENSITY MAPS. CONSEQUENTLY THIS REGION HAS EXTREMELY HIGH TEMPERATURE FACTORS BUT ITS INCLUSION IN THE MODEL WAS REFLECTED BY AN APPRECIABLE DROP IN FREE R FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1691 10 %RANDOM
Rwork0.204 ---
obs-16870 99 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-3.592 Å20 Å20 Å2
2--3.592 Å20 Å2
3----6.691 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 38 128 1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1832
X-RAY DIFFRACTIONp_mcangle_it3.433
X-RAY DIFFRACTIONp_scbond_it2.5162
X-RAY DIFFRACTIONp_scangle_it3.7543
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1360.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.3350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1660.3
X-RAY DIFFRACTIONp_planar_tor27
X-RAY DIFFRACTIONp_staggered_tor18.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.920
X-RAY DIFFRACTIONp_special_tor

+
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://pdbjlvh1.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