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Yorodumi- PDB-4a2j: PR X-Ray structures in agonist conformations reveal two different... -
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-Basic information
Entry | Database: PDB / ID: 4a2j | ||||||
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Title | PR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids | ||||||
Components | PROGESTERONE RECEPTOR | ||||||
Keywords | TRANSCRIPTION / PARTIAL AGONIST | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lusher, S.J. / Raaijmakers, H.C.A. / Bosch, R. / Vu-Pham, D. / McGuire, R. / Oubrie, A. / de Vlieg, J. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2012 Title: X-ray structures of progesterone receptor ligand binding domain in its agonist state reveal differing mechanisms for mixed profiles of 11 beta-substituted steroids. Authors: Lusher, S.J. / Raaijmakers, H.C. / Vu-Pham, D. / Kazemier, B. / Bosch, R. / McGuire, R. / Azevedo, R. / Hamersma, H. / Dechering, K. / Oubrie, A. / van Duin, M. / de Vlieg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a2j.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a2j.ent.gz | 178.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a2j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/4a2j ftp://data.pdbj.org/pub/pdb/validation_reports/a2/4a2j | HTTPS FTP |
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-Related structure data
Related structure data | 4apuC 4a2k C: citing same article (ref.) |
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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
#1: Protein | Mass: 29968.098 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 514-769 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06401 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Nonpolymer details | ASOPRISNIL (AS0): ASOPRISNIL 4-[(11BETA,17BETA)-17-METHOXY-17- (METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN- ...ASOPRISNIL | Sequence details | GLY SER HIS EXPRESSION | |
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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: 2.2 Å3/Da / Density % sol: 44.17 % |
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Crystal grow | pH: 6.5 Details: 20-30% POLYETHYLENE GLYCOL 3350, 0.1 M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 7, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.3 Å / Num. obs: 35323 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.639 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.703 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.68 Å
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