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Yorodumi- PDB-2w8y: RU486 bound to the progesterone receptor in a destabilized agonis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w8y | ||||||
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Title | RU486 bound to the progesterone receptor in a destabilized agonistic conformation | ||||||
Components | PROGESTERONE RECEPTOR | ||||||
Keywords | RECEPTOR / PROGESTERONE RECEPTOR / RU-486 / MIFEPRISTONE | ||||||
Function / homology | Function and homology information glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / estrogen response element binding / Nuclear signaling by ERBB4 ...glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / estrogen response element binding / Nuclear signaling by ERBB4 / intracellular steroid hormone receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / G protein-coupled receptor activity / SUMOylation of intracellular receptors / transcription coactivator binding / Nuclear Receptor transcription pathway / nuclear receptor activity / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / nucleic acid binding / 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 / chromatin / positive regulation of gene expression / 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 / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Raaijmakers, H.C.A. / Versteeg, J. / Uitdehaag, J.C.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: The X-Ray Structure of Ru486 Bound to the Progesterone Receptor in a Destabilized Agonistic Conformation. Authors: Raaijmakers, H.C.A. / Versteegh, J. / Uitdehaag, J.C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w8y.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w8y.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 2w8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w8y ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w8y | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29968.098 Da / Num. of mol.: 2 / Fragment: PR LBD, RESIDUES 678-933 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06401 |
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-Non-polymers , 5 types, 204 molecules
#2: Chemical | ChemComp-486 / |
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#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-NDR / ( |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | NORETHINDRONE (NDR): ALSO KNOWN AS NORETHISTERONE MIFEPRISTONE (486): RU486, 11BETA-4-N, N- ...NORETHINDR |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.46 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 22.5% PEG4000, 0.1M HEPES 6.5, 100 MM LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 17, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47 Å / Num. obs: 45609 / % possible obs: 96.1 % / Observed criterion σ(I): -5 / Redundancy: 3.4 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.2 / % possible all: 77.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→69.67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.412 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. THE DIMETHYLAMINOREMARK A909. IN REALITY WE PROBABLY OBSERVE THE AVERAGE OF AN ENSEMBLE OF SUBTLY DIFFERENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. THE DIMETHYLAMINOREMARK A909. IN REALITY WE PROBABLY OBSERVE THE AVERAGE OF AN ENSEMBLE OF SUBTLY DIFFERENT DIMETHYLANILINE AND MET909 ORIENTATIONS, EACH STERICALLY ALLOWED. FOR THE FINAL REFINEMENT I SET THE OCCUPANCY OF M909 SIDECHAIN TO 0, TO IMPROVE THE FIT OF THE DIMETHYLANILINE TO THE ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→69.67 Å
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