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

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Basic information

Entry
Database: PDB / ID: 2gpu
TitleEstrogen Related Receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen
ComponentsEstrogen-related receptor gamma
KeywordsTRANSCRIPTION / Estrogen related receptor / ERR / ERRg / ESRRG / Nuclear Receptor / Steroid Receptor
Function / homology
Function and homology information


AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / 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 / retinoic acid receptor signaling pathway / estrogen response element binding / 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 / chromatin / regulation of DNA-templated transcription / 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) / Nuclear hormone receptors DNA-binding domain profile. ...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-HYDROXYTAMOXIFEN / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4722
Polymers26,0841
Non-polymers3881
Water5,945330
1
A: Estrogen-related receptor gamma
hetero molecules

A: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9444
Polymers52,1692
Non-polymers7752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)64.01, 64.01, 138.23
Angle α, β, γ (deg.)90, 90, 90
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: Chemical ChemComp-OHT / 4-HYDROXYTAMOXIFEN


Mass: 387.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 36% Peg600, 0.1M tris, 0.1% zwittergent 3-16, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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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: 1.7→50 Å / Num. all: 32660 / Num. obs: 32333 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.9 % / Rmerge(I) obs: 0.07 / Χ2: 0.997
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2
1.7-1.7699.78.50.35131620.51
1.76-1.8310013.70.24732230.541
1.83-1.9110013.70.19331830.682
1.91-2.0210013.80.14732170.862
2.02-2.1410013.80.1132301.088
2.14-2.3110013.70.09332271.318
2.31-2.5499.813.80.07932361.242
2.54-2.9199.613.60.06932681.235
2.91-3.6698.513.10.0632711.276
3.66-5093.311.50.0533161.024

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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
Starting model: 2GP7

2gp7


Resolution: 1.7→46.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.857 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1025 3.2 %RANDOM
Rwork0.18 ---
all0.18 32473 --
obs0.18 32165 99.05 %-
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: 21.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 0 29 330 2310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222032
X-RAY DIFFRACTIONr_bond_other_d0.0010.021886
X-RAY DIFFRACTIONr_angle_refined_deg1.3492.0052774
X-RAY DIFFRACTIONr_angle_other_deg0.81234432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5165265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.42326.3184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24615395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.398155
X-RAY DIFFRACTIONr_chiral_restr0.0670.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022343
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02380
X-RAY DIFFRACTIONr_nbd_refined0.2440.2528
X-RAY DIFFRACTIONr_nbd_other0.1680.21866
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21024
X-RAY DIFFRACTIONr_nbtor_other0.0850.21032
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.229
X-RAY DIFFRACTIONr_mcbond_it1.0441.51656
X-RAY DIFFRACTIONr_mcbond_other0.1851.5493
X-RAY DIFFRACTIONr_mcangle_it1.17522048
X-RAY DIFFRACTIONr_scbond_it2.033893
X-RAY DIFFRACTIONr_scangle_it2.7944.5726
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 65 -
Rwork0.245 2251 -
all-2316 -
obs--99.36 %

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