[English] 日本語
Yorodumi
- PDB-1qkm: HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qkm
TitleHUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN
ComponentsESTROGEN RECEPTOR BETA
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / PHYTO-OESTROGEN / PARTIAL AGONIST
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
GENISTEIN / Estrogen receptor beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Dec 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)28,9962
Polymers28,7261
Non-polymers2701
Water2,504139
1
A: ESTROGEN RECEPTOR BETA
hetero molecules

A: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9934
Polymers57,4522
Non-polymers5402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area3760 Å2
ΔGint-30.4 kcal/mol
Surface area24810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)63.120, 63.120, 250.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsBIOLOGICAL_UNIT: DIMER

-
Components

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


Mass: 28726.092 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH THE PHYTO-OESTROGEN GENISTEIN / Source: (gene. exp.) HOMO SAPIENS (human) / Gene: OESTROGEN RECEPTOR BETA / Plasmid: PLEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GI724 / References: UniProt: Q92731
#2: Chemical ChemComp-GEN / GENISTEIN / 5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4-ONE / 4',5,7-TRIHYDROXYISOFLAVONE / PRUNETOL / GENISTEOL


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.44 Å3/Da / Density % sol: 49 %
Crystal growpH: 8.1
Details: 6-9% (W/V) PEG 6000, 1.6-2.1M NACL, 0.1M TRIS-HCL, PH 8.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
26-9 %(w/v)PEG60001reservoir
31.6-2.1 M1reservoirNaCl
40.1 MTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. obs: 28523 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8 % / Mean I/σ(I) obs: 4 / Rsym value: 0.433 / % possible all: 100
Reflection
*PLUS
Num. measured all: 358818 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.433

-
Processing

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

1ere


Resolution: 1.8→55 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12715 / ESU R Free: 0.12556
Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT. DISCREPANCY BETWEEN REFINEMENT STATISTICS GIVEN ABOVE AND PUBLISHED VALUES ARISE DUE TO A SEQUENCE ERROR THAT HAS ...Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT. DISCREPANCY BETWEEN REFINEMENT STATISTICS GIVEN ABOVE AND PUBLISHED VALUES ARISE DUE TO A SEQUENCE ERROR THAT HAS SUBSEQUENTLY BEEN CORRECTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1441 5 %RANDOM
Rwork0.215 ---
obs-28460 99.7 %-
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.115 Å2-1.138 Å20 Å2
2--3.116 Å20 Å2
3----3.827 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 20 139 1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8512
X-RAY DIFFRACTIONp_mcangle_it2.8473
X-RAY DIFFRACTIONp_scbond_it2.3592
X-RAY DIFFRACTIONp_scangle_it3.7453
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.3610.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1160.3
X-RAY DIFFRACTIONp_planar_tor2.67
X-RAY DIFFRACTIONp_staggered_tor16.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.720
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://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