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- PDB-6k3n: Crystal structure of human estrogen-related receptor gamma ligand... -

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Basic information

Entry
Database: PDB / ID: 6k3n
TitleCrystal structure of human estrogen-related receptor gamma ligand binding domain complex with BPA-monoF
ComponentsEstrogen-related receptor gamma
KeywordsTRANSCRIPTION
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
Chem-CW6 / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMatsushima, A. / Nose, T. / Kakuta, Y.
CitationJournal: Chem.Res.Toxicol. / Year: 2020
Title: Evaluation of the Influence of Halogenation on the Binding of Bisphenol A to the Estrogen-Related Receptor gamma.
Authors: Suyama, K. / Kaneko, S. / Kesamaru, H. / Liu, X. / Matsushima, A. / Kakuta, Y. / Okubo, T. / Kasatani, K. / Nose, T.
History
DepositionMay 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)26,0332
Polymers25,7871
Non-polymers2461
Water82946
1
A: Estrogen-related receptor gamma
hetero molecules

A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0674
Polymers51,5742
Non-polymers4932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2520 Å2
ΔGint-7 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.666, 63.666, 132.212
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: 25787.002 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-CW6 / 2-fluoranyl-4-[2-(4-hydroxyphenyl)propan-2-yl]phenol


Mass: 246.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15FO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05M HEPES, 0.75M sodium citrate, 5% glycerol, pH 7.5,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 19939 / % possible obs: 99.8 % / Redundancy: 13.7 % / Net I/σ(I): 38.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→45.86 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.095 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 968 4.9 %RANDOM
Rwork0.2108 ---
obs0.2129 18971 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.32 Å2 / Biso mean: 30.543 Å2 / Biso min: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.97→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 18 46 1869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021885
X-RAY DIFFRACTIONr_angle_refined_deg2.072.0032559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1682680
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45315364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.908155
X-RAY DIFFRACTIONr_chiral_restr0.1370.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211375
LS refinement shellResolution: 1.969→2.021 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 66 -
Rwork0.286 1151 -
all-1217 -
obs--95.38 %

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