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- PDB-2e2r: Crystal structure of human estrogen-related receptor gamma ligand... -

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Basic information

Entry
Database: PDB / ID: 2e2r
TitleCrystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol A
ComponentsEstrogen-related receptor gamma
KeywordsTRANSCRIPTION / ERR gamma / BPA / nuclear receptor
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
4,4'-PROPANE-2,2-DIYLDIPHENOL / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMatsushima, A. / Kakuta, Y. / Teramoto, T. / Koshiba, T. / Kimura, M. / Shimohigashi, Y.
CitationJournal: J.Biochem.(Tokyo) / Year: 2007
Title: Structural Evidence for Endocrine Disruptor Bisphenol A Binding to Human Nuclear Receptor ERR{gamma}
Authors: Matsushima, A. / Kakuta, Y. / Teramoto, T. / Koshiba, T. / Liu, X. / Okada, H. / Tokunaga, T. / Kawabata, S. / Kimura, M. / Shimohigashi, Y.
History
DepositionNov 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE This difference is based on Reference 3 in the database, ERR3_HUMAN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1165
Polymers27,6111
Non-polymers5054
Water6,972387
1
A: Estrogen-related receptor gamma
hetero molecules

A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,23110
Polymers55,2222
Non-polymers1,0098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)64.046, 64.046, 136.871
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 / Estrogen receptor-related protein 3 / ERR gamma-2


Mass: 27611.137 Da / Num. of mol.: 1 / Fragment: ligand binding domain, residues 232-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62508
#2: Chemical ChemComp-2OH / 4,4'-PROPANE-2,2-DIYLDIPHENOL / 4,4'-ISOPROPYLIDENEDIPHENOL / BISPHENOL A


Mass: 228.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05M HEPES, 0.75M sodium citrate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 18, 2006
RadiationMonochromator: Si 111 Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→28.06 Å / Num. all: 36414 / Num. obs: 36414 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 40.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 8.2 / Num. unique all: 3729 / Rsym value: 0.349 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
BBSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S9Q

1s9q


Resolution: 1.6→28.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.357 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19666 1921 5 %RANDOM
Rwork0.16934 ---
all0.17071 36414 --
obs0.17071 36414 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.709 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 35 387 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222027
X-RAY DIFFRACTIONr_bond_other_d0.0020.021904
X-RAY DIFFRACTIONr_angle_refined_deg1.3332.0012775
X-RAY DIFFRACTIONr_angle_other_deg0.82234499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1235273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022224
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02359
X-RAY DIFFRACTIONr_nbd_refined0.220.2476
X-RAY DIFFRACTIONr_nbd_other0.2280.22197
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.51218
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33622002
X-RAY DIFFRACTIONr_scbond_it2.1163809
X-RAY DIFFRACTIONr_scangle_it3.4794.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 159
Rwork0.209 2611

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