[English] 日本語
Yorodumi
- PDB-1hj1: RAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hj1
TitleRAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PURE ANTIOESTROGEN ICI164,384
ComponentsOESTROGEN RECEPTOR BETA
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / OESTROGEN / ANTAGONIST
Function / homology
Function and homology information


negative regulation of behavior / cellular response to magnetism / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / response to bisphenol A / response to insecticide / estradiol binding / amygdala development / response to human chorionic gonadotropin ...negative regulation of behavior / cellular response to magnetism / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / response to bisphenol A / response to insecticide / estradiol binding / amygdala development / response to human chorionic gonadotropin / Extra-nuclear estrogen signaling / hormone-mediated apoptotic signaling pathway / epithelial cell maturation involved in prostate gland development / Sertoli cell proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / prostate gland development / response to genistein / steroid hormone binding / Nuclear Receptor transcription pathway / Sertoli cell development / negative regulation of androgen receptor signaling pathway / 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 / nuclear estrogen receptor activity / hypothalamus development / negative regulation of feeding behavior / heterocyclic compound binding / female gonad development / uterus development / response to testosterone / vagina development / response to dexamethasone / : / androgen receptor signaling pathway / negative regulation of reactive oxygen species metabolic process / estrogen response element binding / behavioral fear response / nuclear receptor-mediated steroid hormone signaling pathway / ovarian follicle development / estrous cycle / estrogen receptor signaling pathway / response to hormone / steroid binding / cerebellum development / positive regulation of DNA-binding transcription factor activity / epithelial cell proliferation / response to activity / response to nicotine / negative regulation of smooth muscle cell proliferation / promoter-specific chromatin binding / cellular response to estradiol stimulus / response to nutrient levels / brain development / : / protein-DNA complex / response to estrogen / nuclear receptor activity / male gonad development / neuron migration / negative regulation of epithelial cell proliferation / vasodilation / cellular response to xenobiotic stimulus / response to estradiol / regulation of cell population proliferation / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / perikaryon / negative regulation of neuron apoptotic process / sequence-specific DNA binding / response to ethanol / learning or memory / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / regulation of transcription by RNA polymerase II / chromatin / 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 ...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-AOE / NICKEL (II) ION / PARA-MERCURY-BENZENESULFONIC ACID / Estrogen receptor beta
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPike, A.C.W. / Brzozowski, A.M. / Carlquist, M.
Citation
Journal: Structure / Year: 2001
Title: Structural Insights Into the Mode of Action of a Pure Antiestrogen
Authors: Pike, A.C.W. / Brzozowski, A.M. / Walton, J. / Hubbard, R.E. / Thorsell, A.G. / Li, Y.L. / Gustafsson, J.A. / Carlquist, M.
#1: Journal: Biochem.Soc.Trans. / Year: 2001
Title: Structural Aspects of Agonism and Antagonism in the Oestrogen Receptor
Authors: Pike, A.C. / Brzozowski, A.M. / Walton, J. / Hubbard, R.E. / Bonn, T. / Gustafsson, J.A. / Carlquist, M.
History
DepositionJan 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6875
Polymers28,6861
Non-polymers1,0014
Water82946
1
A: OESTROGEN RECEPTOR BETA
hetero molecules

A: OESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,37410
Polymers57,3722
Non-polymers2,0028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)60.380, 82.670, 106.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsBIOMOLECULEHOMODIMER

-
Components

#1: Protein OESTROGEN 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 FULL ANTAGONIST ICI164,384 / 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-AOE / N-BUTYL-11-[(7R,8R,9S,13S,14S,17S)-3,17-DIHYDROXY-13-METHYL-7,8,9,11,12,13,14,15,16,17-DECAHYDRO-6H-CYCLOPENTA[A]PHENANTHREN-7-YL]-N-METHYLUNDECANAMIDE


Mass: 525.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H55NO3 / Comment: antagonist*YM
#3: Chemical ChemComp-PMB / PARA-MERCURY-BENZENESULFONIC ACID


Mass: 357.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5HgO3S
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5
Details: 7.0% (W/V) PEG 2000 MONOMETHYL ETHER 0.0035M NICKEL CHLORIDE 0.035M TRIS-HCL, PH 8.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
27 %(w/v)PEG2000 MME1reservoir
33.5 mM1reservoirNiCl2
410 %(v/v)dioxane1reservoir
535 mMTris-HCl1reservoirpH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9464
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12201 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 48.5 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.326 / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 185069 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4phasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QKN

1qkn


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31611 / ESU R Free: 0.22821
Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT REFINEMENT. TEMPERATURE FACTORS OF HG OF RESIDUE PMB A1437 REFINED ANISOTROPICALLY. ISOTROPIC MODEL USED FOR REMAINING ...Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT REFINEMENT. TEMPERATURE FACTORS OF HG OF RESIDUE PMB A1437 REFINED ANISOTROPICALLY. ISOTROPIC MODEL USED FOR REMAINING ATOMS. RESIDUES AFTER LYS435 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS. PCMBS MOLECULE COVALENTLY BOUND (PMB) TO CYS289
RfactorNum. reflection% reflectionSelection details
Rfree0.25051 587 5 %RANDOM
Rwork0.21966 ---
obs-11328 98.2 %-
Displacement parametersBiso mean: 53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1582 0 51 46 1679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8392
X-RAY DIFFRACTIONp_mcangle_it2.9283
X-RAY DIFFRACTIONp_scbond_it2.0752
X-RAY DIFFRACTIONp_scangle_it3.3013
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1210.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.1840.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1480.3
X-RAY DIFFRACTIONp_planar_tor1.77
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3520
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.21966
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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