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- PDB-2gpo: Estrogen Related Receptor-gamma ligand binding domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 2gpo
TitleEstrogen Related Receptor-gamma ligand binding domain complexed with a synthetic peptide from RIP140
Components
  • Estrogen-related receptor gamma
  • Nuclear receptor-interacting protein 1
KeywordsTRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor / RIP140
Function / homology
Function and homology information


ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / lipid storage / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / nuclear glucocorticoid receptor binding / nuclear steroid receptor activity / histone deacetylase complex / retinoic acid receptor signaling pathway / estrogen response element binding ...ovarian follicle rupture / AF-2 domain binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / lipid storage / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / nuclear glucocorticoid receptor binding / nuclear steroid receptor activity / histone deacetylase complex / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / SUMOylation of transcription cofactors / cellular response to estradiol stimulus / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / fibrillar center / histone deacetylase binding / Nuclear Receptor transcription pathway / circadian rhythm / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / regulation of DNA-templated transcription / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Oestrogen-related receptor ...Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / 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
Nuclear receptor-interacting protein 1 / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Osband-miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: X-ray crystal structures of the estrogen-related receptor-gamma ligand binding domain in three functional states reveal the molecular basis of small molecule regulation.
Authors: Wang, L. / Zuercher, W.J. / Consler, T.G. / Lambert, M.H. / Miller, A.B. / Orband-Miller, L.A. / McKee, D.D. / Willson, T.M. / Nolte, R.T.
History
DepositionApr 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 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
C: Nuclear receptor-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)28,9182
Polymers28,9182
Non-polymers00
Water5,080282
1
A: Estrogen-related receptor gamma
C: Nuclear receptor-interacting protein 1

A: Estrogen-related receptor gamma
C: Nuclear receptor-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)57,8354
Polymers57,8354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)64.315, 64.315, 139.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 26084.373 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain (Residues 229-458)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRG / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62508
#2: Protein/peptide Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 2833.291 Da / Num. of mol.: 1 / Fragment: LXXLL Motif (Residues 366-390) / Source method: obtained synthetically
Details: Chemically synthesized. Occurs naturally in Homo Sapiens (humans).
References: UniProt: P48552
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14% PEG 3350 0.2M sodium formate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 22078 / Num. obs: 22078 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.057 / Χ2: 1.003
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.379 / Num. measured obs: 2145 / Χ2: 1.089 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→47.14 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.434 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 713 3.2 %RANDOM
Rwork0.181 ---
all0.182 22144 --
obs0.182 22011 99.75 %-
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: 29.603 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 0 282 2216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221972
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9932676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.425249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25626.23585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63315387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.916155
X-RAY DIFFRACTIONr_chiral_restr0.0750.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021448
X-RAY DIFFRACTIONr_nbd_refined0.2040.2974
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.216
X-RAY DIFFRACTIONr_mcbond_it0.9261.51275
X-RAY DIFFRACTIONr_mcangle_it1.33121985
X-RAY DIFFRACTIONr_scbond_it2.143794
X-RAY DIFFRACTIONr_scangle_it3.2924.5691
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 58 -
Rwork0.229 1516 -
all-1574 -
obs--99.31 %

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