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- PDB-6i65: Crystal structure of human ERRg LBD in complex with 4-iso-propylphenol -

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Basic information

Entry
Database: PDB / ID: 6i65
TitleCrystal structure of human ERRg LBD in complex with 4-iso-propylphenol
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
4-propan-2-ylphenol / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)27,4372
Polymers27,3011
Non-polymers1361
Water5,873326
1
A: Estrogen-related receptor gamma
hetero molecules

A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8744
Polymers54,6022
Non-polymers2722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2420 Å2
ΔGint-6 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.434, 64.434, 137.275
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) / References: UniProt: P62508
#2: Chemical ChemComp-H3Z / 4-propan-2-ylphenol


Mass: 136.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0-100 mM Sodium acetat 100 mM Tris 23-26% PEG8000

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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 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.5→46.98 Å / Num. obs: 47226 / % possible obs: 100 % / Redundancy: 12.2 % / Rrim(I) all: 0.054 / Net I/σ(I): 23.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 6758 / Rrim(I) all: 0.559 / % possible all: 100

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Processing

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

2zbs


Resolution: 1.5→46.978 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.1975 4488 5.08 %
Rwork0.1728 --
obs0.174 88387 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→46.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 10 326 2095
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061899
X-RAY DIFFRACTIONf_angle_d0.7722597
X-RAY DIFFRACTIONf_dihedral_angle_d3.2342007
X-RAY DIFFRACTIONf_chiral_restr0.044308
X-RAY DIFFRACTIONf_plane_restr0.005329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.22211500.24252768X-RAY DIFFRACTION100
1.5171-1.53490.23051410.24072830X-RAY DIFFRACTION100
1.5349-1.55360.26961800.22982729X-RAY DIFFRACTION100
1.5536-1.57330.30621590.22442809X-RAY DIFFRACTION100
1.5733-1.5940.24231440.21652773X-RAY DIFFRACTION100
1.594-1.61580.24761660.21592833X-RAY DIFFRACTION100
1.6158-1.63890.2561260.21352749X-RAY DIFFRACTION100
1.6389-1.66340.23111370.2052822X-RAY DIFFRACTION100
1.6634-1.68940.22771370.19832843X-RAY DIFFRACTION100
1.6894-1.71710.23461440.19852796X-RAY DIFFRACTION100
1.7171-1.74670.21311380.19142810X-RAY DIFFRACTION100
1.7467-1.77850.23921490.19812810X-RAY DIFFRACTION100
1.7785-1.81270.20961370.20262786X-RAY DIFFRACTION100
1.8127-1.84970.21721390.20392826X-RAY DIFFRACTION100
1.8497-1.88990.2051550.19282802X-RAY DIFFRACTION100
1.8899-1.93380.22231450.19822788X-RAY DIFFRACTION100
1.9338-1.98220.20611400.20162807X-RAY DIFFRACTION100
1.9822-2.03580.2411420.18922794X-RAY DIFFRACTION100
2.0358-2.09570.19321780.18572789X-RAY DIFFRACTION100
2.0957-2.16330.24221720.18352785X-RAY DIFFRACTION100
2.1633-2.24070.20721460.17252770X-RAY DIFFRACTION100
2.2407-2.33040.23461350.18052839X-RAY DIFFRACTION100
2.3304-2.43640.20791850.17732735X-RAY DIFFRACTION100
2.4364-2.56490.17821500.17032812X-RAY DIFFRACTION100
2.5649-2.72560.2121580.16962788X-RAY DIFFRACTION100
2.7256-2.9360.20321410.16752824X-RAY DIFFRACTION100
2.936-3.23140.16661470.16212792X-RAY DIFFRACTION100
3.2314-3.69880.16211610.15212782X-RAY DIFFRACTION100
3.6988-4.65940.15741460.13412795X-RAY DIFFRACTION100
4.6594-47.00050.18711400.16372813X-RAY DIFFRACTION100

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