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- PDB-6i61: Crystal structure of human ERRg LBD in complex with bisphenol-B -

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Basic information

Entry
Database: PDB / ID: 6i61
TitleCrystal structure of human ERRg LBD in complex with bisphenol-B
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 / 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 ...AF-2 domain binding / nuclear steroid receptor activity / estrogen response element binding / retinoic acid receptor 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 / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus
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 / Double treble clef zinc finger, C4 type ...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 / 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
bisphenol-B / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0668
Polymers27,3011
Non-polymers7657
Water3,909217
1
A: Estrogen-related receptor gamma
hetero molecules

A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,13116
Polymers54,6022
Non-polymers1,53014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4990 Å2
ΔGint-12 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.030, 64.030, 135.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 / Plasmid: pDB-His-GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62508
#2: Chemical ChemComp-H3W / bisphenol-B


Mass: 242.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0-100 mM Sodium Acetate 100 mM Tris 23-26% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.65→42.94 Å / Num. obs: 34719 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rrim(I) all: 0.092 / Net I/σ(I): 13.7
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2510 / Rrim(I) all: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZBS

2zbs


Resolution: 1.65→37.638 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.86
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 1736 5 %random
Rwork0.1851 ---
obs0.1868 34714 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→37.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 52 217 2010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061893
X-RAY DIFFRACTIONf_angle_d0.8062579
X-RAY DIFFRACTIONf_dihedral_angle_d3.1051568
X-RAY DIFFRACTIONf_chiral_restr0.047301
X-RAY DIFFRACTIONf_plane_restr0.005325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69850.27111400.24712672X-RAY DIFFRACTION100
1.6985-1.75330.2351420.23642690X-RAY DIFFRACTION100
1.7533-1.8160.26581420.2172708X-RAY DIFFRACTION100
1.816-1.88870.23641430.21232715X-RAY DIFFRACTION100
1.8887-1.97470.25131420.21142695X-RAY DIFFRACTION100
1.9747-2.07880.21511440.19172731X-RAY DIFFRACTION100
2.0788-2.2090.23821430.18092728X-RAY DIFFRACTION100
2.209-2.37950.20531450.18622744X-RAY DIFFRACTION100
2.3795-2.61890.21821430.19422728X-RAY DIFFRACTION100
2.6189-2.99780.22351460.18162773X-RAY DIFFRACTION100
2.9978-3.77630.2011490.16882829X-RAY DIFFRACTION100

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