[English] 日本語
Yorodumi
- PDB-4oar: Progesterone receptor with bound ulipristal acetate and a peptide... -

+
Open data


ID or keywords:

Loading...

-
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 / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / ovulation from ovarian follicle / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation ...glandular epithelial cell maturation / Loss of MECP2 binding ability to the NCoR/SMRT complex / tertiary branching involved in mammary gland duct morphogenesis / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / ovulation from ovarian follicle / paracrine signaling / maintenance of protein location in nucleus / regulation of epithelial cell proliferation / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / lung alveolus development / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / steroid binding / lactation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / cerebellum development / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / enzyme activator activity / HDACs deacetylate histones / SUMOylation of intracellular receptors / Downregulation of SMAD2/3:SMAD4 transcriptional activity / transcription coactivator binding / PPARA activates gene expression / G protein-coupled receptor activity / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / nuclear matrix / nuclear receptor activity / HCMV Early Events / transcription corepressor activity / cell-cell signaling / response to estradiol / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / 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. / Myb domain / SANT domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...Progesterone receptor / Progesterone receptor / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SANT domain profile. / Myb domain / SANT 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 -

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more