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Yorodumi- PDB-4ypq: Crystal structure of the ROR(gamma)t ligand binding domain in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ypq | ||||||
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Title | Crystal structure of the ROR(gamma)t ligand binding domain in complex with 4-(1-(2-chloro-6-(trifluoromethyl)benzoyl)-1H-indazol-3-yl)benzoic acid | ||||||
Components | Nuclear receptor ROR-gamma | ||||||
Keywords | TRANSCRIPTION / nuclear receptor ligand binding domain | ||||||
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: 2.32 Å | ||||||
Authors | Leysen, S. / Scheepstra, M. / van Almen, G.C. / Ottmann, C. / Brunsveld, L. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Identification of an allosteric binding site for ROR gamma t inhibition. Authors: Scheepstra, M. / Leysen, S. / van Almen, G.C. / Miller, J.R. / Piesvaux, J. / Kutilek, V. / van Eenennaam, H. / Zhang, H. / Barr, K. / Nagpal, S. / Soisson, S.M. / Kornienko, M. / Wiley, K. ...Authors: Scheepstra, M. / Leysen, S. / van Almen, G.C. / Miller, J.R. / Piesvaux, J. / Kutilek, V. / van Eenennaam, H. / Zhang, H. / Barr, K. / Nagpal, S. / Soisson, S.M. / Kornienko, M. / Wiley, K. / Elsen, N. / Sharma, S. / Correll, C.C. / Trotter, B.W. / van der Stelt, M. / Oubrie, A. / Ottmann, C. / Parthasarathy, G. / Brunsveld, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ypq.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ypq.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 4ypq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/4ypq ftp://data.pdbj.org/pub/pdb/validation_reports/yp/4ypq | HTTPS FTP |
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-Related structure data
Related structure data | 5c4oC 5c4sC 5c4tC 5c4uC 4nieS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28307.824 Da / Num. of mol.: 1 / Fragment: UNP residues 265-507 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) / Strain (production host): Nico321(DE3) / References: UniProt: P51449 |
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#2: Chemical | ChemComp-4F1 / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium chloride, 0.1M Tris pH 8.5, 7% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.5 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→35.47 Å / Num. obs: 16884 / % possible obs: 100 % / Redundancy: 11.7 % / Rsym value: 0.121 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.886 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NIE Resolution: 2.32→35.465 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.67 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→35.465 Å
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Refine LS restraints |
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LS refinement shell |
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