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- PDB-6fzu: RORGT (264-518;C455S) IN COMPLEX WITH THE FRAGMENT ("CPD-1") AND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fzu | ||||||
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Title | RORGT (264-518;C455S) IN COMPLEX WITH THE FRAGMENT ("CPD-1") AND RIP140 PEPTIDE AT 1.80A | ||||||
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![]() | TRANSCRIPTION / FBS / NUCLEAR HORMONE RECEPTOR / LIGAND-BINDING DOMAIN / INVERSE AGONIST / SIGNALING PROTEIN | ||||||
Function / homology | ![]() ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear glucocorticoid receptor binding / Peyer's patch development ...ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / nuclear glucocorticoid receptor binding / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / 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 estrogen receptor binding / nuclear 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 / nucleolus / regulation of transcription by RNA polymerase II / 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: Optimizing a Weakly Binding Fragment into a Potent ROR gamma t Inverse Agonist with Efficacy in an in Vivo Inflammation Model. Authors: Carcache, D.A. / Vulpetti, A. / Kallen, J. / Mattes, H. / Orain, D. / Stringer, R. / Vangrevelinghe, E. / Wolf, R.M. / Kaupmann, K. / Ottl, J. / Dawson, J. / Cooke, N.G. / Hoegenauer, K. / ...Authors: Carcache, D.A. / Vulpetti, A. / Kallen, J. / Mattes, H. / Orain, D. / Stringer, R. / Vangrevelinghe, E. / Wolf, R.M. / Kaupmann, K. / Ottl, J. / Dawson, J. / Cooke, N.G. / Hoegenauer, K. / Billich, A. / Wagner, J. / Guntermann, C. / 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 | ![]() | 121.6 KB | Display | ![]() |
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PDB format | ![]() | 92.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 459.2 KB | Display | |
Data in XML | ![]() | 22.4 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g05C ![]() 6g07C ![]() 5ntiS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29739.316 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 22% PEG3350, 0.2M ammonium acetate, 0.1M bis-TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2015 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.8 Å / Num. obs: 46451 / % possible obs: 96.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 33.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.072 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.652 / Rrim(I) all: 0.699 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NTI Resolution: 1.8→19.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.284 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1636 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.148 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 62.83 Å2 / Biso mean: 30.206 Å2 / Biso min: 12.86 Å2
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Refinement step | Cycle: final / Resolution: 1.8→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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