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- PDB-5ntn: Structural states of RORgt: X-ray elucidation of molecular mechan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ntn | ||||||
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Title | Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds | ||||||
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![]() | SIGNALING PROTEIN / nuclear hormone receptor / ligand-binding domain / agonist | ||||||
Function / homology | ![]() ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / Peyer's patch development ...ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / histone deacetylase complex / regulation of glucose metabolic process / lymph node development / adipose tissue development / nuclear retinoid X receptor binding / xenobiotic metabolic process / SUMOylation of transcription cofactors / cellular response to estradiol stimulus / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / fibrillar center / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Nuclear Receptor transcription pathway / circadian rhythm / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription coactivator activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kallen, J. | ||||||
![]() | ![]() Title: Structural States of ROR gamma t: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds. Authors: Kallen, J. / Izaac, A. / Be, C. / Arista, L. / Orain, D. / Kaupmann, K. / Guntermann, C. / Hoegenauer, K. / Hintermann, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.1 KB | Display | ![]() |
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PDB format | ![]() | 184.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ntiC ![]() 5ntkC ![]() 5ntpC ![]() 5ntqC ![]() 5ntwC ![]() 5nu1C ![]() 1s0xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29739.316 Da / Num. of mol.: 4 / Fragment: C-terminal domain, ligand binding domain / Mutation: C455S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2319.615 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-98H / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.24 % / Mosaicity: 0.584 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG 3350, 0.04M NaFormate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 28, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.90013 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→20 Å / Num. obs: 77514 / % possible obs: 89.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Χ2: 1.048 / Net I/σ(I): 13.4 / Num. measured all: 280258 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1s0x Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.339 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1982 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.159 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.61 Å2 / Biso mean: 28.5 Å2 / Biso min: 12.31 Å2
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Refinement step | Cycle: final / Resolution: 1.9→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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