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- PDB-6i62: Crystal structure of human ERRg LBD in complex with HPTE -

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Basic information

Entry
Database: PDB / ID: 6i62
TitleCrystal structure of human ERRg LBD in complex with HPTE
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
4,4'-(2,2,2-trichloroethane-1,1-diyl)diphenol / 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)27,1952
Polymers26,8771
Non-polymers3181
Water4,450247
1
A: Estrogen-related receptor gamma
hetero molecules

A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3904
Polymers53,7552
Non-polymers6352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2630 Å2
ΔGint-8 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.198, 64.198, 136.792
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: 26877.301 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-27N / 4,4'-(2,2,2-trichloroethane-1,1-diyl)diphenol


Mass: 317.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11Cl3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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→46.81 Å / Num. obs: 34911 / % possible obs: 99.3 % / Redundancy: 8.9 % / Rrim(I) all: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 5048 / Rrim(I) all: 0.634 / % 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→45.394 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 19.99
RfactorNum. reflection% reflection
Rfree0.1997 3267 5.01 %
Rwork0.175 --
obs0.1762 65262 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→45.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 19 247 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061885
X-RAY DIFFRACTIONf_angle_d0.8892576
X-RAY DIFFRACTIONf_dihedral_angle_d1.9591587
X-RAY DIFFRACTIONf_chiral_restr0.054304
X-RAY DIFFRACTIONf_plane_restr0.005326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67470.29341210.27032741X-RAY DIFFRACTION100
1.6747-1.70080.25511350.25152683X-RAY DIFFRACTION100
1.7008-1.72870.29861460.24522719X-RAY DIFFRACTION100
1.7287-1.75850.31271100.24062708X-RAY DIFFRACTION100
1.7585-1.79050.24621480.2282761X-RAY DIFFRACTION100
1.7905-1.8250.24191310.21152710X-RAY DIFFRACTION100
1.825-1.86220.26631550.2122687X-RAY DIFFRACTION100
1.8622-1.90270.19611240.20772713X-RAY DIFFRACTION100
1.9027-1.9470.2471340.20522748X-RAY DIFFRACTION100
1.947-1.99570.24851650.20542669X-RAY DIFFRACTION100
1.9957-2.04960.20391730.18932667X-RAY DIFFRACTION100
2.0496-2.10990.24791380.18462748X-RAY DIFFRACTION100
2.1099-2.1780.21211340.17452670X-RAY DIFFRACTION100
2.178-2.25590.22161340.18172743X-RAY DIFFRACTION100
2.2559-2.34620.21051500.19382648X-RAY DIFFRACTION100
2.3462-2.4530.18661460.19212719X-RAY DIFFRACTION99
2.453-2.58230.19161490.17742682X-RAY DIFFRACTION99
2.5823-2.7440.22161670.17672656X-RAY DIFFRACTION99
2.744-2.95590.19791360.17152680X-RAY DIFFRACTION99
2.9559-3.25330.15721520.16142682X-RAY DIFFRACTION99
3.2533-3.72380.18691330.14762680X-RAY DIFFRACTION99
3.7238-4.69090.16931420.13812657X-RAY DIFFRACTION98

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