[English] 日本語
Yorodumi- PDB-6t4u: ROR(gamma)t ligand binding domain in complex with 20-alpha-hydrox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t4u | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | ROR(gamma)t ligand binding domain in complex with 20-alpha-hydroxycholesterol and allosteric ligand MRL871 | ||||||||||||
Components | Nuclear receptor ROR-gamma | ||||||||||||
Keywords | GENE REGULATION / Nuclear Receptor / Allosteric / Inverse Agonist / Inhibitor | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | de Vries, R.M.J.M. / Meijer, F.A. / Brunsveld, L. | ||||||||||||
Funding support | Netherlands, 3items
| ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6t4u.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6t4u.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 6t4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/6t4u ftp://data.pdbj.org/pub/pdb/validation_reports/t4/6t4u | HTTPS FTP |
---|
-Related structure data
Related structure data | 6t4gC 6t4iC 6t4jC 6t4kC 6t4tC 6t4wC 6t4xC 6t4yC 6t50C 6tlqC 6tltC 6salS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28071.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449 |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-HCD / ( |
#4: Chemical | ChemComp-4F1 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.31 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: none - crystallized in storage buffer upon evaporation |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033208 Å | ||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength | Wavelength: 1.033208 Å / Relative weight: 1 | ||||||||||||
Reflection | Resolution: 2→105.94 Å / Num. obs: 46074 / % possible obs: 98.2 % / Redundancy: 27.5 % / Biso Wilson estimate: 41.4 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.015 / Rrim(I) all: 0.088 / Net I/σ(I): 23.3 | ||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SAL Resolution: 2→54.26 Å / SU ML: 0.2917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2432 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→54.26 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 5.52293358861 Å / Origin y: -39.8788887671 Å / Origin z: -4.72844556577 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: (chain A and resseq 268:507) |