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Yorodumi- PDB-1nhz: Crystal Structure of the Antagonist Form of Glucocorticoid Receptor -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nhz | ||||||
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Title | Crystal Structure of the Antagonist Form of Glucocorticoid Receptor | ||||||
Components | GLUCOCORTICOID RECEPTOR | ||||||
Keywords | Hormone receptor / PROTEIN-LIGAND COMPLEX / ANTI PARALLEL ALPHA HELIX SANDWICH | ||||||
Function / homology | Function and homology information Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis / maternal behavior / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / adrenal gland development / regulation of gluconeogenesis / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to dexamethasone stimulus / nuclear receptor-mediated steroid hormone signaling pathway / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / TBP-class protein binding / positive regulation of miRNA transcription / SUMOylation of intracellular receptors / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Hsp90 protein binding / Nuclear Receptor transcription pathway / nuclear receptor activity / spindle / Regulation of RUNX2 expression and activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / Circadian Clock / chromatin organization / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / mitochondrial matrix / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / negative regulation of DNA-templated transcription / centrosome / synapse / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / protein kinase binding / apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. ...Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / Gustafsson, J.-A. / Carlstedt-Duke, J. / Carlquist, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The Three-dimensional Structures of Antagonistic and Agonistic Forms of the Glucocorticoid Receptor Ligand-binding Domain: RU-486 INDUCES A TRANSCONFORMATION THAT LEADS TO ACTIVE ANTAGONISM. Authors: Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / ...Authors: Kauppi, B. / Jakob, C. / Farnegardh, M. / Yang, J. / Ahola, H. / Alarcon, M. / Calles, K. / Engstrom, O. / Harlan, J. / Muchmore, S. / Ramqvist, A.-K. / Thorell, S. / Ohman, L. / Greer, J. / Gustafsson, J.-A. / Carlstedt-Duke, J. / Carlquist, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nhz.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nhz.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 1nhz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nhz_validation.pdf.gz | 784.7 KB | Display | wwPDB validaton report |
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Full document | 1nhz_full_validation.pdf.gz | 793.4 KB | Display | |
Data in XML | 1nhz_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1nhz_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/1nhz ftp://data.pdbj.org/pub/pdb/validation_reports/nh/1nhz | HTTPS FTP |
-Related 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32155.072 Da / Num. of mol.: 1 Fragment: residue 500-777, hinge and steroid binding domains Mutation: N517D, F602S, C638D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P04150 | ||
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#2: Chemical | ChemComp-486 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.04 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: PEG 8000, 1, 6-hexanediol, NaSCN, Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.26 Å / Num. all: 14833 / Num. obs: 14815 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.035 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 6.1 / Num. unique all: 2064 / Rsym value: 0.121 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.106 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→62.02 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / SU B: 6.11 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.253 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.433 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→62.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å |