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- PDB-6hl1: Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hl1 | |||||||||
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Title | Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide and CDCA | |||||||||
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![]() | NUCLEAR PROTEIN / Activator / DNA-binding / Receptor / Repressor / Complex | |||||||||
Function / homology | ![]() regulation of urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / : / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid ...regulation of urea metabolic process / nuclear receptor-mediated bile acid signaling pathway / chenodeoxycholic acid binding / positive regulation of phosphatidic acid biosynthetic process / positive regulation of glutamate metabolic process / positive regulation of ammonia assimilation cycle / : / regulation of low-density lipoprotein particle clearance / intracellular triglyceride homeostasis / cellular response to bile acid / negative regulation of very-low-density lipoprotein particle remodeling / negative regulation of interleukin-1 production / regulation of bile acid biosynthetic process / regulation of insulin secretion involved in cellular response to glucose stimulus / : / toll-like receptor 9 signaling pathway / intracellular receptor signaling pathway / negative regulation of monocyte chemotactic protein-1 production / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / bile acid binding / cell-cell junction assembly / bile acid signaling pathway / cellular response to fatty acid / negative regulation of interleukin-2 production / regulation of cholesterol metabolic process / positive regulation of interleukin-17 production / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / Synthesis of bile acids and bile salts / fatty acid homeostasis / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / positive regulation of insulin receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Recycling of bile acids and salts / Notch signaling pathway / positive regulation of adipose tissue development / transcription coregulator binding / cholesterol homeostasis / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / euchromatin / PPARA activates gene expression / negative regulation of inflammatory response / Nuclear Receptor transcription pathway / nuclear receptor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kudlinzki, D. / Merk, D. / Linhard, V.L. / Saxena, K. / Schubert-Zsilavecz, M. / Schwalbe, H. | |||||||||
![]() | ![]() Title: Molecular tuning of farnesoid X receptor partial agonism. Authors: Merk, D. / Sreeramulu, S. / Kudlinzki, D. / Saxena, K. / Linhard, V. / Gande, S.L. / Hiller, F. / Lamers, C. / Nilsson, E. / Aagaard, A. / Wissler, L. / Dekker, N. / Bamberg, K. / Schubert- ...Authors: Merk, D. / Sreeramulu, S. / Kudlinzki, D. / Saxena, K. / Linhard, V. / Gande, S.L. / Hiller, F. / Lamers, C. / Nilsson, E. / Aagaard, A. / Wissler, L. / Dekker, N. / Bamberg, K. / Schubert-Zsilavecz, M. / Schwalbe, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.6 KB | Display | ![]() |
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PDB format | ![]() | 92 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 700.5 KB | Display | ![]() |
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Full document | ![]() | 703.1 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hl0C ![]() 4qe6 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: 27159.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein Domain with bound CDCA / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1593.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Chemical | ChemComp-JN3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 39.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM Ca(CH3COO)2, 10 mM DTT, 25-30% PEG 3350, 100 mM Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98004 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→34.236 Å / Num. obs: 29422 / % possible obs: 95.4 % / Redundancy: 6.74 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.049 / Net I/σ(I): 24.06 |
Reflection shell | Resolution: 1.599→1.7 Å / Redundancy: 4.58 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3739 / CC1/2: 0.736 / Rrim(I) all: 0.846 / % possible all: 75.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QE6 ![]() 4qe6 Resolution: 1.599→34.236 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.599→34.236 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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