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- PDB-6t4y: ROR(gamma)t ligand binding domain in complex with 25-hydroxychole... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t4y | ||||||||||||
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Title | ROR(gamma)t ligand binding domain in complex with 25-hydroxycholesterol and allosteric ligand MRL871 | ||||||||||||
![]() | Nuclear receptor ROR-gamma | ||||||||||||
![]() | GENE REGULATION / Nuclear Receptor / Allosteric / Inverse Agonist / Inhibitor | ||||||||||||
Function / homology | ![]() T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / 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 ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / 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 / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | de Vries, R.M.J.M. / Meijer, F.A. / Brunsveld, L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cooperativity between the orthosteric and allosteric ligand binding sites of ROR gamma t. Authors: de Vries, R.M.J.M. / Meijer, F.A. / Doveston, R.G. / Leijten-van de Gevel, I.A. / Brunsveld, L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.5 KB | Display | ![]() |
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PDB format | ![]() | 94.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1017.1 KB | Display | ![]() |
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Full document | ![]() | 1018.5 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t4gC ![]() 6t4iC ![]() 6t4jC ![]() 6t4kC ![]() 6t4tC ![]() 6t4uC ![]() 6t4wC ![]() 6t4xC ![]() 6t50C ![]() 6tlqC ![]() 6tltC ![]() 6salS 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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Unit cell |
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Components
#1: Protein | Mass: 30514.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HC3 / |
#3: Chemical | ChemComp-4F1 / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.6M AmSO4 + 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2019 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 1.95→105.04 Å / Num. obs: 50467 / % possible obs: 100 % / Redundancy: 38.9 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.012 / Rrim(I) all: 0.073 / Net I/σ(I): 28.5 | ||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6SAL Resolution: 1.95→93.972 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.71
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.06 Å2 / Biso mean: 61.0044 Å2 / Biso min: 36.05 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→93.972 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 5.6762 Å / Origin y: -39.8368 Å / Origin z: -4.6117 Å
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Refinement TLS group | Selection details: (chain A and resseq 267:507) |