+Open data
-Basic information
Entry | Database: PDB / ID: 4zjr | ||||||
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Title | RORgamma in complex with inverse agonist 48 | ||||||
Components | Nuclear receptor ROR-gamma | ||||||
Keywords | TRANSCRIPTION / RORgamma ligand binding domain / Inverse agonist | ||||||
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: 2.702 Å | ||||||
Authors | Marcotte, D.J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2015 Title: Discovery of biaryl carboxylamides as potent ROR gamma inverse agonists. Authors: Chao, J. / Enyedy, I. / Van Vloten, K. / Marcotte, D. / Guertin, K. / Hutchings, R. / Powell, N. / Jones, H. / Bohnert, T. / Peng, C.C. / Silvian, L. / Hong, V.S. / Little, K. / Banerjee, D. ...Authors: Chao, J. / Enyedy, I. / Van Vloten, K. / Marcotte, D. / Guertin, K. / Hutchings, R. / Powell, N. / Jones, H. / Bohnert, T. / Peng, C.C. / Silvian, L. / Hong, V.S. / Little, K. / Banerjee, D. / Peng, L. / Taveras, A. / Viney, J.L. / Fontenot, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zjr.cif.gz | 188.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zjr.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zjr_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4zjr_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4zjr_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 4zjr_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zjr ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zjr | HTTPS FTP |
-Related structure data
Related structure data | 4zjwC 3b0wS 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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Unit cell |
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Details | SEC confirms monomeric state |
-Components
#1: Protein | Mass: 26160.232 Da / Num. of mol.: 4 / Fragment: ligand binding domain (UNP Residues 265-487) 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): BL21 (DE3) / References: UniProt: P51449 #2: Chemical | ChemComp-4P3 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.0M Sodium Acetate, 0.2M Sodium Chloride, 0.1M TRIS pH 8.0 PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→85.225 Å / Num. all: 38563 / Num. obs: 38506 / % possible obs: 99.7 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.085 / Rrim(I) all: 0.233 / Net I/av σ(I): 2.642 / Net I/σ(I): 15.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3B0W Resolution: 2.702→85.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.54 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.59 Å2 / Biso mean: 50.016 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 2.702→85.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.702→2.772 Å / Total num. of bins used: 20
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