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- PDB-1s9p: crystal structure of the ligand-binding domain of the estrogen-re... -

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Basic information

Entry
Database: PDB / ID: 1s9p
Titlecrystal structure of the ligand-binding domain of the estrogen-related receptor gamma in complex with diethylstilbestrol
ComponentsEstrogen-related receptor gamma
KeywordsTRANSCRIPTION / ligand-binding domain / antagonist complex
Function / homology
Function and homology information


Nuclear Receptor transcription pathway / nuclear steroid receptor activity / estrogen response element binding / retinoic acid receptor signaling pathway / steroid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear receptor activity / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / calmodulin binding ...Nuclear Receptor transcription pathway / nuclear steroid receptor activity / estrogen response element binding / retinoic acid receptor signaling pathway / steroid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear receptor activity / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / calmodulin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion 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
DIETHYLSTILBESTROL / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsGreschik, H. / Flaig, R. / Renaud, J.P. / Moras, D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis for the Deactivation of the Estrogen-related Receptor {gamma} by Diethylstilbestrol or 4-Hydroxytamoxifen and Determinants of Selectivity.
Authors: Greschik, H. / Flaig, R. / Renaud, J.P. / Moras, D.
History
DepositionFeb 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
C: Estrogen-related receptor gamma
D: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2218
Polymers103,1484
Non-polymers1,0734
Water3,711206
1
A: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1114
Polymers51,5742
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-8 kcal/mol
Surface area20250 Å2
MethodPISA
2
C: Estrogen-related receptor gamma
D: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1114
Polymers51,5742
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Estrogen-related receptor gamma
B: Estrogen-related receptor gamma
hetero molecules

C: Estrogen-related receptor gamma
D: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2218
Polymers103,1484
Non-polymers1,0734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area10200 Å2
ΔGint-29 kcal/mol
Surface area38220 Å2
MethodPISA
4
B: Estrogen-related receptor gamma
hetero molecules

C: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1114
Polymers51,5742
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area3000 Å2
ΔGint-18 kcal/mol
Surface area21130 Å2
MethodPISA
5
A: Estrogen-related receptor gamma
D: Estrogen-related receptor gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1114
Polymers51,5742
Non-polymers5372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-16 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.999, 77.460, 95.773
Angle α, β, γ (deg.)90.00, 97.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Estrogen-related receptor gamma / Estrogen receptor related protein 3 / ERR gamma-2


Mass: 25787.002 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ESRRG, NR3B3, ERRG2, ERR3, KIAA0832 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62509
#2: Chemical
ChemComp-DES / DIETHYLSTILBESTROL


Mass: 268.350 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H20O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 297 K / pH: 8
Details: PEG3350, NaOAc, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2002 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.13→45 Å / Num. obs: 57942 / % possible obs: 99 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.039 / Net I/σ(I): 46.6
Reflection shellResolution: 2.13→2.21 Å / Mean I/σ(I) obs: 9.7 / Rsym value: 0.159 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KV6

1kv6


Resolution: 2.13→29.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 768655.75 / Data cutoff high rms absF: 768655.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2930 5.1 %RANDOM
Rwork0.226 ---
obs0.226 57722 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 43.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å2-0.24 Å2
2--9.44 Å20 Å2
3----7.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-30 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.13→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 80 206 7129
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.14
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.13→2.21 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.292 281 4.9 %
Rwork0.266 5419 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMDES.TOP
X-RAY DIFFRACTION3DES.PAR

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