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- PDB-2p7g: X-ray Structure of Estrogen Related Receptor g in complex with Bi... -

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Basic information

Entry
Database: PDB / ID: 2p7g
TitleX-ray Structure of Estrogen Related Receptor g in complex with Bisphenol A.
ComponentsEstrogen-related receptor gamma
KeywordsHORMONE RECEPTOR / three layered alpha helical sandwich
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'-PROPANE-2,2-DIYLDIPHENOL / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbad, M.C.
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2008
Title: Structural determination of estrogen-related receptor gamma in the presence of phenol derivative compounds.
Authors: Abad, M.C. / Askari, H. / O'Neill, J. / Klinger, A.L. / Milligan, C. / Lewandowski, F. / Springer, B. / Spurlino, J. / Rentzeperis, D.
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

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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)28,6383
Polymers28,3871
Non-polymers2512
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.063, 64.063, 136.484
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: 28386.941 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: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P62508
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22.6% polyethylene glycol 4000, 0.1M Tris, pH 8.5 and 0.2M Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 6, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→68.5 Å / Num. obs: 17455 / Redundancy: 2.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3595 / Rsym value: 0.133

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
SAINTdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1KV6

1kv6


Resolution: 2.1→68.5 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1700 -random
Rwork0.215 ---
all0.21 17322 --
obs-17174 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.1→68.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 18 172 1951
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.06264
X-RAY DIFFRACTIONc_bond_d0.005773

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