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- PDB-7kxf: CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C (NHIS-RORGT(24... -
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Basic information
Entry | Database: PDB / ID: 7kxf | ||||||
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Title | CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C (NHIS-RORGT(244-487)-L6-SRC1(678-692)) IN COMPLEX WITH {3,5-DICHLORO-4-[4-METHOXY-3-(PROPAN-2-YL)PHENOXY]PHENYL}METHANOL | ||||||
![]() | Nuclear receptor ROR-gamma, Nuclear receptor coactivator 1 chimera | ||||||
![]() | TRANSFERASE/Agonist / RORGT / NUCLEAR HORMONE RECEPTOR / LIGAND-BINDING DOMAIN / INVERSE AGONIST / TRANSFERASE-Agonist complex | ||||||
Function / homology | ![]() ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / labyrinthine layer morphogenesis ...ligand-activated transcription factor activity / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / labyrinthine layer morphogenesis / negative regulation of thymocyte apoptotic process / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of fat cell differentiation / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / estrous cycle / Synthesis of bile acids and bile salts / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / Endogenous sterols / lymph node development / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / adipose tissue development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RORA activates gene expression / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / xenobiotic metabolic process / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / mRNA transcription by RNA polymerase II / response to progesterone / nuclear receptor binding / hippocampus development / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / circadian regulation of gene expression / Heme signaling / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / Transcriptional regulation of white adipocyte differentiation / Cytoprotection by HMOX1 / RNA polymerase II transcription regulator complex / cerebral cortex development / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / HATs acetylate histones / transcription regulator complex / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sack, J. | ||||||
![]() | ![]() Title: Substituted diaryl ether compounds as retinoic acid-related orphan Receptor-gamma t (ROR gamma t) agonists. Authors: Ruan, Z. / Park, P.K. / Wei, D. / Purandare, A. / Wan, H. / O'Malley, D. / Stachura, S. / Perez, H. / Cavallaro, C.L. / Weigelt, C.A. / Sack, J.S. / Ruzanov, M. / Khan, J. / Gururajan, M. / ...Authors: Ruan, Z. / Park, P.K. / Wei, D. / Purandare, A. / Wan, H. / O'Malley, D. / Stachura, S. / Perez, H. / Cavallaro, C.L. / Weigelt, C.A. / Sack, J.S. / Ruzanov, M. / Khan, J. / Gururajan, M. / Wong, J.J. / Huang, Y. / Yarde, M. / Li, Z. / Chen, C. / Sun, H. / Borowski, V. / Xie, J.H. / Anthony, M. / Agler, M. / Fink, B.E. / Harikrishnan, L.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 71.2 KB | Display | ![]() |
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PDB format | ![]() | 49.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kxdC ![]() 7kxeC ![]() 6u25S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32886.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P51449, UniProt: Q15788, histone acetyltransferase |
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#2: Chemical | ChemComp-Z7I / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 22% PEG3350, 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→78.37 Å / Num. obs: 16687 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Biso Wilson estimate: 35.36 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.14→2.26 Å / Redundancy: 13 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2042 / % possible all: 83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6u25 Resolution: 2.141→57.22 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.184
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Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.141→57.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.142→2.16 Å
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