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- PDB-5va0: Glucocorticoid Receptor DNA Binding Domain in complex with AP-1 r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5va0 | ||||||
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Title | Glucocorticoid Receptor DNA Binding Domain in complex with AP-1 response element from VCAM-1 Promoter | ||||||
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![]() | transcription/dna / Nuclear Receptor / Transcription Factor / DNA Binding / Development / Protein-DNA complex / transcription-dna complex | ||||||
Function / homology | ![]() 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 / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / 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 / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / SUMOylation of intracellular receptors / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / spindle / Regulation of RUNX2 expression and activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / 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 / apoptotic process / synapse / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Weikum, E.R. / Ortlund, E.A. | ||||||
![]() | ![]() Title: Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes. Authors: Weikum, E.R. / de Vera, I.M.S. / Nwachukwu, J.C. / Hudson, W.H. / Nettles, K.W. / Kojetin, D.J. / Ortlund, E.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 41.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 436.9 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5va7C ![]() 4hn5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8047.488 Da / Num. of mol.: 2 / Fragment: unp residues 84-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | | Mass: 4883.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | | Mass: 4914.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.05 M Na Cacodylate (pH 7), 5 mM MgCl2, 1 mM Spermine, and 2 % t-Butanol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 13, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.28→50 Å / Num. obs: 18797 / % possible obs: 96.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 41.19 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.056 / Rrim(I) all: 0.145 / Χ2: 1.398 / Net I/σ(I): 7.3 / Num. measured all: 130117 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4HN5 Resolution: 2.295→34.483 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.18 Å2 / Biso mean: 42.9987 Å2 / Biso min: 22.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.295→34.483 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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