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

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Basic information

Entry
Database: PDB / ID: 1vjb
Titlecrystal structure of the ligand-binding domain of the estrogen-related receptor gamma in complex with 4-hydroxytamoxifen
ComponentsEstrogen-related receptor gamma
KeywordsTRANSCRIPTION / ligand-binding domain / ANTAGONIST COMPLEX
Function / homology
Function and homology information


Nuclear Receptor transcription pathway / AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / steroid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Nuclear Receptor transcription pathway / nuclear receptor activity ...Nuclear Receptor transcription pathway / AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / steroid binding / RNA polymerase II transcription regulatory region sequence-specific DNA 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 / calmodulin binding / 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 DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / 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 / 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 / Estrogen-related receptor gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 3, 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 1.3Jun 13, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity_name_com.name / _entity_src_gen.gene_src_common_name ..._entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type
Revision 1.4Aug 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5494
Polymers56,7742
Non-polymers7752
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-15 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.624, 74.624, 144.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Estrogen-related receptor gamma / / Estrogen receptor-related protein 3 / Nuclear receptor subfamily 3 group B member 3


Mass: 28386.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Esrrg, Err3, Kiaa0832, Nr3b3 / Production host: Escherichia coli (E. coli) / References: UniProt: P62509, UniProt: P62508*PLUS
#2: Chemical ChemComp-OHT / 4-HYDROXYTAMOXIFEN / Afimoxifene


Mass: 387.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H29NO2

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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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9804
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 22, 2002 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 3.2→45 Å / Num. obs: 8116 / % possible obs: 99 % / Redundancy: 4.6 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.051 / Net I/σ(I): 30.9
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.229 / % possible all: 100

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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: 3.2→24.13 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1212173.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.275 372 4.6 %RANDOM
Rwork0.256 ---
obs0.256 8063 99.2 %-
all-8116 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.11 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 70.4 Å2
Baniso -1Baniso -2Baniso -3
1-15.31 Å27.46 Å20 Å2
2--15.31 Å20 Å2
3----30.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.47 Å
Luzzati d res low-25 Å
Luzzati sigma a0.43 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 3.2→24.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 58 0 3246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.82
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
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: 3.2→3.4 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 61 4.6 %
Rwork0.294 1265 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION24OHT.PAR4OHT.TOP

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