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- PDB-4oar: Progesterone receptor with bound ulipristal acetate and a peptide... -

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Basic information

Entry
Database: PDB / ID: 4oar
TitleProgesterone receptor with bound ulipristal acetate and a peptide from the co-repressor SMRT
Components
  • Peptide from Nuclear receptor corepressor 2
  • Progesterone receptor
KeywordsTRANSCRIPTION/Peptide / PROGESTERONE RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / WOMEN HEALTH / CONTRACEPTION / TRANSCRIPTION-Peptide complex
Function / homology
Function and homology information


glandular epithelial cell maturation / Loss of MECP2 binding ability to the NCoR/SMRT complex / tertiary branching involved in mammary gland duct morphogenesis / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / Notch binding ...glandular epithelial cell maturation / Loss of MECP2 binding ability to the NCoR/SMRT complex / tertiary branching involved in mammary gland duct morphogenesis / negative regulation of androgen receptor signaling pathway / regulation of cellular ketone metabolic process / nuclear glucocorticoid receptor binding / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / Notch binding / nuclear steroid receptor activity / lung alveolus development / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / progesterone receptor signaling pathway / Regulation of MECP2 expression and activity / estrous cycle / estrogen response element binding / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / Nuclear signaling by ERBB4 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to organonitrogen compound / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / transcription repressor complex / lactation / steroid binding / Regulation of lipid metabolism by PPARalpha / cerebellum development / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / G protein-coupled receptor activity / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SUMOylation of intracellular receptors / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / histone deacetylase binding / transcription corepressor activity / nuclear receptor activity / response to estradiol / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / nucleic acid binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Progesterone receptor / Progesterone receptor / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain ...Progesterone receptor / Progesterone receptor / N-CoR, GPS2-interacting domain / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Retinoid X Receptor / Retinoid X Receptor / Homeobox-like domain superfamily / 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
Chem-2S0 / Progesterone receptor / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsPetit-Topin, I. / Fay, M.R. / Resche-Rigon, M. / Ulmann, A. / Gainer, E. / Rafestin-Oblin, M.-E. / Fagart, J.
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2014
Title: Molecular determinants of the recognition of ulipristal acetate by oxo-steroid receptors.
Authors: Petit-Topin, I. / Fay, M. / Resche-Rigon, M. / Ulmann, A. / Gainer, E. / Rafestin-Oblin, M.E. / Fagart, J.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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: Progesterone receptor
B: Peptide from Nuclear receptor corepressor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0873
Polymers31,6112
Non-polymers4761
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-9 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.180, 87.180, 90.910
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 Progesterone receptor / / PR / Nuclear receptor subfamily 3 group C member 3


Mass: 29698.762 Da / Num. of mol.: 1 / Fragment: Steroid-binding Region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C3, PGR / Plasmid: pGexhPRLBD / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON PLUS (DE3) RIL / References: UniProt: P06401
#2: Protein/peptide Peptide from Nuclear receptor corepressor 2 / / SMRT PEPTIDE


Mass: 1912.345 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2346-2362 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y618
#3: Chemical ChemComp-2S0 / [(8S,11R,13S,14S,17R)-17-acetyl-11-[4-(dimethylamino)phenyl]-13-methyl-3-oxo-1,2,6,7,8,11,12,14,15,16-decahydrocyclopen ta[a]phenanthren-17-yl] acetate / ulipristal acetate / Ulipristal acetate


Mass: 475.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37NO4 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG3350, Tris,HCl 50mM, NaCl 400mM, 10% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 13, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→43.59 Å / Num. obs: 13598 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.65 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.084 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.41 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.05 / Rsym value: 0.325 / % possible all: 67.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OVH

2ovh


Resolution: 2.41→43.59 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2465515.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 680 5 %RANDOM
Rwork0.211 ---
obs0.211 13598 84.8 %-
all-16033 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.95 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0.41 Å20 Å2
2--0.36 Å20 Å2
3----0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.41→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 35 42 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg2.5
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_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.522.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.41→2.51 Å /
RfactorNum. reflection
Rfree0.3015 67
Rwork0.2791 -

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