[English] 日本語
Yorodumi
- PDB-6i66: Crystal structure of human ERRg LBD in complex with 4-sec-butylphenol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i66
TitleCrystal structure of human ERRg LBD in complex with 4-sec-butylphenol
ComponentsEstrogen-related receptor gamma
KeywordsNUCLEAR PROTEIN / transcription factor nuclear receptor endocrine disruptor
Function / homology
Function and homology information


AF-2 domain binding / nuclear steroid receptor activity / estrogen response element binding / retinoic acid receptor signaling pathway / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis ...AF-2 domain binding / nuclear steroid receptor activity / estrogen response element binding / retinoic acid receptor signaling pathway / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding
Similarity search - Function
Oestrogen-related receptor / Retinoic acid receptor / 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) ...Oestrogen-related receptor / Retinoic acid receptor / 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
4-[(2~{R})-butan-2-yl]phenol / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDelfosse, V. / Blanc, P. / Bourguet, W.
Funding support France, 1items
OrganizationGrant numberCountry
Plan Cancer ASC16007FSA France
CitationJournal: Cell.Mol.Life Sci. / Year: 2019
Title: Insights into the activation mechanism of human estrogen-related receptor gamma by environmental endocrine disruptors.
Authors: Thouennon, E. / Delfosse, V. / Bailly, R. / Blanc, P. / Boulahtouf, A. / Grimaldi, M. / Barducci, A. / Bourguet, W. / Balaguer, P.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6354
Polymers27,3011
Non-polymers3343
Water4,954275
1
A: Estrogen-related receptor gamma
hetero molecules

A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2708
Polymers54,6022
Non-polymers6696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3400 Å2
ΔGint-7 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.350, 64.350, 135.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Estrogen-related receptor gamma / ERR gamma-2 / Estrogen receptor-related protein 3 / Nuclear receptor subfamily 3 group B member 3


Mass: 27300.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3 / Production host: Escherichia coli (E. coli) / References: UniProt: P62508
#2: Chemical ChemComp-H4Q / 4-[(2~{R})-butan-2-yl]phenol


Mass: 150.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0-100 mM Sodium acetate 100 mM Tris 23-26% PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.6→58.15 Å / Num. obs: 71858 / % possible obs: 100 % / Redundancy: 12.2 % / Rrim(I) all: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 5511 / Rrim(I) all: 0.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZBS

2zbs


Resolution: 1.6→46.706 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 20.27
RfactorNum. reflection% reflection
Rfree0.2068 3603 5.01 %
Rwork0.1741 --
obs0.1757 71858 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→46.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 23 275 2045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061911
X-RAY DIFFRACTIONf_angle_d0.9872612
X-RAY DIFFRACTIONf_dihedral_angle_d12.597739
X-RAY DIFFRACTIONf_chiral_restr0.037309
X-RAY DIFFRACTIONf_plane_restr0.005330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62110.30441470.24352581X-RAY DIFFRACTION100
1.6211-1.64330.26691380.23942634X-RAY DIFFRACTION100
1.6433-1.66680.2541420.22922605X-RAY DIFFRACTION100
1.6668-1.69170.2571620.21882659X-RAY DIFFRACTION100
1.6917-1.71810.23141320.21242601X-RAY DIFFRACTION100
1.7181-1.74630.31741280.22122646X-RAY DIFFRACTION100
1.7463-1.77640.27491370.22152617X-RAY DIFFRACTION100
1.7764-1.80870.23981160.21752619X-RAY DIFFRACTION100
1.8087-1.84350.26511440.21112640X-RAY DIFFRACTION100
1.8435-1.88110.21311250.20092639X-RAY DIFFRACTION100
1.8811-1.9220.23741320.20882640X-RAY DIFFRACTION100
1.922-1.96670.29391400.19862619X-RAY DIFFRACTION100
1.9667-2.01590.27421640.20532619X-RAY DIFFRACTION100
2.0159-2.07040.23131370.18462613X-RAY DIFFRACTION100
2.0704-2.13130.22341250.18062636X-RAY DIFFRACTION100
2.1313-2.20010.18861570.17412605X-RAY DIFFRACTION100
2.2001-2.27880.19851700.17612615X-RAY DIFFRACTION100
2.2788-2.370.23151230.1882631X-RAY DIFFRACTION100
2.37-2.47790.24061560.17922625X-RAY DIFFRACTION100
2.4779-2.60850.24251490.18162615X-RAY DIFFRACTION100
2.6085-2.77190.16111250.18142636X-RAY DIFFRACTION100
2.7719-2.98590.20751460.16532603X-RAY DIFFRACTION100
2.9859-3.28630.22791130.15972651X-RAY DIFFRACTION100
3.2863-3.76160.17191290.14942642X-RAY DIFFRACTION100
3.7616-4.73860.161300.1362624X-RAY DIFFRACTION100
4.7386-46.72550.16581360.16832640X-RAY DIFFRACTION100

+
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