Entry | Database: PDB / ID: 4wvd |
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Title | Identification of a novel FXR ligand that regulates metabolism |
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Components | - Bile acid receptor
- Nuclear receptor corepressor 1
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Keywords | TRANSCRIPTION / AF-2 helix / ligand binding pocket / three-layer helical sandwich / TRANSCRIPTION REGULATOR FXR / BAR / NR1H4 / bile acid receptor / NHR / nuclear receptor / corepressor / Transcription regulation |
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Function / homology | Function and homology information
NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 ...NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / 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 androgen receptor signaling pathway / 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 / negative regulation of JNK cascade / bile acid metabolic process / nitrogen catabolite activation of transcription from RNA polymerase II promoter / negative regulation of glycolytic process / cell-cell junction assembly / bile acid binding / bile acid signaling pathway / nuclear thyroid hormone receptor binding / cellular response to fatty acid / regulation of cholesterol metabolic process / negative regulation of fatty acid metabolic process / negative regulation of interleukin-2 production / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / intracellular glucose homeostasis / positive regulation of interleukin-17 production / locomotor rhythm / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / histone deacetylase complex / Regulation of MECP2 expression and activity / negative regulation of tumor necrosis factor production / negative regulation of type II interferon production / Synthesis of bile acids and bile salts / negative regulation of tumor necrosis factor-mediated signaling pathway / spindle assembly / 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 / Nuclear signaling by ERBB4 / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Notch signaling pathway / positive regulation of adipose tissue development / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / negative regulation of miRNA transcription / cholesterol homeostasis / transcription coregulator binding / nuclear receptor binding / HDACs deacetylate histones / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / SUMOylation of intracellular receptors / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / RNA polymerase II transcription regulator complex / transcription corepressor activity / nuclear receptor activity / Circadian Clock / chromatin organization / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / defense response to bacterium / inflammatory responseSimilarity search - Function N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Bile acid receptor, ligand binding domain / Thyroid hormone receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / Bile acid receptor, ligand binding domain / Thyroid hormone receptor / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / : / Retinoid X Receptor / Retinoid X Receptor / Homeobox-like domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly AlphaSimilarity search - Domain/homology |
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Biological species | Homo sapiens (human) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å |
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Authors | Wang, R. / Li, Y. |
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Funding support | China, 4items Organization | Grant number | Country |
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National Basic Research Program of China | 973 Program: 2012CB910104 | China | National Natural Science Foundation of China | 81273567 | China | National Natural Science Foundation of China | 31270776 | China | Programme of Introducing Talents of Discipline to Universities | B12001 | China |
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Citation | Journal: Nat Commun / Year: 2013 Title: The antiparasitic drug ivermectin is a novel FXR ligand that regulates metabolism. Authors: Jin, L. / Feng, X. / Rong, H. / Pan, Z. / Inaba, Y. / Qiu, L. / Zheng, W. / Lin, S. / Wang, R. / Wang, Z. / Wang, S. / Liu, H. / Li, S. / Xie, W. / Li, Y. |
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History | Deposition | Nov 5, 2014 | Deposition site: RCSB / Processing site: PDBJ |
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Supersession | Feb 11, 2015 | ID: 4II6 |
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Revision 1.0 | Feb 11, 2015 | Provider: repository / Type: Initial release |
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Revision 1.1 | Sep 2, 2015 | Group: Data collection |
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Revision 1.2 | Sep 27, 2017 | Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation |
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Revision 1.3 | Mar 20, 2024 | Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name |
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