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Yorodumi- PDB-7yxn: Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yxn | |||||||||||||||
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Title | Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment | |||||||||||||||
Components |
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Keywords | NUCLEAR PROTEIN / Nuclear Receptor / Transcription Factor / Dexamethasone | |||||||||||||||
Function / homology | Function and homology information bile acid and bile salt transport / peroxisome proliferator activated receptor binding / transcription regulator inhibitor activity / nuclear thyroid hormone receptor binding / nuclear retinoid X receptor binding / animal organ regeneration / estrogen response element binding / response to glucose / nuclear receptor-mediated steroid hormone signaling pathway / Notch signaling pathway ...bile acid and bile salt transport / peroxisome proliferator activated receptor binding / transcription regulator inhibitor activity / nuclear thyroid hormone receptor binding / nuclear retinoid X receptor binding / animal organ regeneration / estrogen response element binding / response to glucose / nuclear receptor-mediated steroid hormone signaling pathway / Notch signaling pathway / cholesterol metabolic process / circadian regulation of gene expression / Nuclear Receptor transcription pathway / circadian rhythm / positive regulation of insulin secretion / negative regulation of DNA-binding transcription factor activity / response to organic cyclic compound / nuclear receptor activity / transcription corepressor activity / response to ethanol / protein domain specific binding / negative regulation of gene expression / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | unidentified (others) Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | |||||||||||||||
Authors | Jimenez-Panizo, A. / Estebanez-Perpina, E. / Fuentes-Prior, P. | |||||||||||||||
Funding support | Spain, 4items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities. Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Tettey, T.T. / Fettweis, G. / Abella, M. / Anton, R. / Johnson, T.A. / Kim, S. / Schiltz, R.L. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / ...Authors: Jimenez-Panizo, A. / Alegre-Marti, A. / Tettey, T.T. / Fettweis, G. / Abella, M. / Anton, R. / Johnson, T.A. / Kim, S. / Schiltz, R.L. / Nunez-Barrios, I. / Font-Diaz, J. / Caelles, C. / Valledor, A.F. / Perez, P. / Rojas, A.M. / Fernandez-Recio, J. / Presman, D.M. / Hager, G.L. / Fuentes-Prior, P. / Estebanez-Perpina, E. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yxn.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yxn.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 7yxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yxn_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7yxn_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yxn_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 7yxn_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/7yxn ftp://data.pdbj.org/pub/pdb/validation_reports/yx/7yxn | HTTPS FTP |
-Related structure data
Related structure data | 7yxcC 7yxdC 7yxoC 7yxpC 7yxrC 5ufsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 28835.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X8XLE9 #2: Protein/peptide | Mass: 1204.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15466 #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4 Å3/Da / Density % sol: 69.26 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→94.81 Å / Num. obs: 33009 / % possible obs: 96.8 % / Redundancy: 2.9 % / CC1/2: 0.994 / Rpim(I) all: 0.051 / Rrim(I) all: 0.074 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.46→2.56 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3799 / CC1/2: 0.317 / Rpim(I) all: 0.725 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UFS Resolution: 2.46→94.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.749 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 179.89 Å2 / Biso mean: 68.274 Å2 / Biso min: 29.69 Å2
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Refinement step | Cycle: final / Resolution: 2.46→94.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.46→2.52 Å / Rfactor Rfree error: 0
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