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Nuclear receptor ligand-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Nuclear receptor ligand-binding domain [ 48507]
Superfamily:   Nuclear receptor ligand-binding domain [ 48508]
Families:   Nuclear receptor ligand-binding domain [ 48509] (33)


Superfamily statistics
Genomes (171) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,550 20,765 148
Proteins 8,431 20,607 148


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.00015170Least InformativeDirect
Biological Process (BP)regulation of gene expression0.0000010980Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.00000012770.000000000000003734Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00000013650Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.00000031320Moderately InformativeDirect
Biological Process (BP)regulation of molecular function0.0032930.8884Moderately InformativeInherited
Biological Process (BP)negative regulation of molecular function0.015960.05502InformativeInherited
Biological Process (BP)negative regulation of sequence-specific DNA binding transcription factor activity0.0000004260.0000000005113Highly InformativeDirect
Molecular Function (MF)binding0.0000039840Least InformativeDirect
Molecular Function (MF)nucleic acid binding0.051920.05366Moderately InformativeInherited
Molecular Function (MF)DNA binding0.000081610InformativeDirect
Molecular Function (MF)transcription factor activity, sequence-specific DNA binding0.000011520InformativeDirect
Molecular Function (MF)signal transducer activity0.00068780InformativeDirect
Molecular Function (MF)molecular transducer activity0.00049540InformativeDirect
Molecular Function (MF)transcription factor activity, transcription factor binding0.00000012520Highly InformativeDirect
Molecular Function (MF)hormone binding0.0000093380Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.003350Least InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0.000006375 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000000001459 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0003493 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000003994 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000001201 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.3862 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.5647 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) reproduction 0.00000000001274 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.00000174 Moderately Informative Direct
Biological Process (BP) cell communication 0.00000004183 Moderately Informative Direct
Biological Process (BP) response to endogenous stimulus 0 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000000000000007296 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000000000000003734 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) single organism signaling 0.00004727 Moderately Informative Direct
Biological Process (BP) animal organ development 0.0000000000218 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00000000004684 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.000000000003268 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.0000000000003647 Moderately Informative Direct
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.3578 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.8884 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.166 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8069 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2483 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.02975 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.01082 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.5201 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.7279 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.6748 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7179 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02194 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.1738 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.8943 Moderately Informative Inherited
Biological Process (BP) tissue development 0.3252 Moderately Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.0000985 Informative Direct
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.0000001136 Informative Direct
Biological Process (BP) central nervous system development 0.000004842 Informative Direct
Biological Process (BP) behavior 0.00006407 Informative Direct
Biological Process (BP) response to temperature stimulus 0.00000005868 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.0000000004834 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0 Informative Direct
Biological Process (BP) positive regulation of gene expression 0 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.00023 Informative Direct
Biological Process (BP) regulation of hormone levels 0.0003758 Informative Direct
Biological Process (BP) response to organic cyclic compound 0 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.00000000001943 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0002221 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0 Informative Direct
Biological Process (BP) regulation of protein localization 0.00008733 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00003729 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.000000004393 Informative Direct
Biological Process (BP) single organism reproductive process 0.0000000199 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.0000195 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.0000004778 Informative Direct
Biological Process (BP) regulation of secretion 0.0005132 Informative Direct
Biological Process (BP) reproductive system development 0.00000006364 Informative Direct
Biological Process (BP) cellular response to lipid 0 Informative Direct
Biological Process (BP) regulation of peptide transport 0.0005801 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.0007755 Informative Direct
Biological Process (BP) negative regulation of cell death 0.0323 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.0273 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.07497 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.2737 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 1 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.00664 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.1715 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.009402 Informative Inherited
Biological Process (BP) positive regulation of developmental process 1 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.7471 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.05502 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 1 Informative Inherited
Biological Process (BP) response to acid chemical 0.03481 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1343 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.593 Informative Inherited
Biological Process (BP) embryo development 0.8986 Informative Inherited
Biological Process (BP) epithelium development 0.06339 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) generation of neurons 0.9852 Informative Inherited
Biological Process (BP) organic acid transport 0.004015 Informative Inherited
Biological Process (BP) lipid localization 0.002901 Informative Inherited
Biological Process (BP) anion transport 0.1808 Informative Inherited
Biological Process (BP) positive regulation of transport 1 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.7571 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.2721 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.6927 Informative Inherited
Biological Process (BP) cation homeostasis 0.971 Informative Inherited
Biological Process (BP) inorganic ion homeostasis 1 Informative Inherited
Biological Process (BP) cellular chemical homeostasis 1 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.02263 Informative Inherited
Biological Process (BP) xenobiotic metabolic process 0.0000006655 Highly Informative Direct
Biological Process (BP) sex differentiation 0.00000001907 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0002675 Highly Informative Direct
Biological Process (BP) response to heat 0.000000000007095 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0.00000000005448 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.0000001076 Highly Informative Direct
Biological Process (BP) monocarboxylic acid transport 0.00000443 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.0004386 Highly Informative Direct
Biological Process (BP) forebrain development 0.000000001502 Highly Informative Direct
Biological Process (BP) response to retinoic acid 0.00000000039 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.0000000005113 Highly Informative Direct
Biological Process (BP) response to estrogen 0.000000000002044 Highly Informative Direct
Biological Process (BP) multi-multicellular organism process 0.0000001198 Highly Informative Direct
Biological Process (BP) positive regulation of transcription from RNA polymerase II promoter 0.000002954 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 0.000001695 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.0000001993 Highly Informative Direct
Biological Process (BP) regulation of oxidoreductase activity 0.00006034 Highly Informative Direct
Biological Process (BP) response to glucocorticoid 0.00000000000002436 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 0 Highly Informative Direct
Biological Process (BP) response to ketone 0.0000009734 Highly Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.00008098 Highly Informative Direct
Biological Process (BP) negative regulation of apoptotic process 0.2028 Highly Informative Inherited
Biological Process (BP) positive regulation of reactive oxygen species metabolic process 0.1811 Highly Informative Inherited
Biological Process (BP) positive regulation of lipid metabolic process 0.006355 Highly Informative Inherited
Biological Process (BP) response to peptide hormone 1 Highly Informative Inherited
Biological Process (BP) cellular response to organonitrogen compound 0.09258 Highly Informative Inherited
Biological Process (BP) regulation of steroid biosynthetic process 0.169 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell proliferation 0.02717 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 1 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.7617 Highly Informative Inherited
Biological Process (BP) circadian rhythm 0.03745 Highly Informative Inherited
Biological Process (BP) multicellular organismal homeostasis 0.07502 Highly Informative Inherited
Biological Process (BP) regulation of reactive oxygen species biosynthetic process 0.02362 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.0361 Highly Informative Inherited
Biological Process (BP) regulation of carbohydrate biosynthetic process 0.1002 Highly Informative Inherited
Biological Process (BP) lipid modification 0.001935 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.02476 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 0.1288 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.5346 Highly Informative Inherited
Biological Process (BP) neuron development 0.9023 Highly Informative Inherited
Biological Process (BP) regulation of lipid localization 0.002656 Highly Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.002847 Highly Informative Inherited
Biological Process (BP) response to carbohydrate 0.8875 Highly Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 0.6052 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 1 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0.2648 Highly Informative Inherited
Biological Process (BP) cellular polysaccharide biosynthetic process 0.8244 Highly Informative Inherited
Biological Process (BP) energy reserve metabolic process 0.003316 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.05366 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.7301 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.0643 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) signal transducer activity 0 Informative Direct
Molecular Function (MF) receptor binding 0.0000000000102 Informative Direct
Molecular Function (MF) carboxylic acid binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.000000000004124 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.0002067 Highly Informative Direct
Molecular Function (MF) steroid binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) drug binding 0.00000000005248 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.0005633 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) hormone binding 0 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.000002952 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0002783 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.08112 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) protein complex 0.9501 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cell projection 1 Moderately Informative Inherited
Cellular Component (CC) ribosome 0.07704 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.004164 Moderately Informative Inherited
Cellular Component (CC) nuclear part 1 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.00000009815 Informative Direct
Cellular Component (CC) neuron projection 0.1006 Informative Inherited
Cellular Component (CC) plasma membrane bounded cell projection part 0.8938 Informative Inherited
Cellular Component (CC) chromatin 0.00000000002794 Highly Informative Direct
Cellular Component (CC) dendrite 0.0003965 Highly Informative Direct
Cellular Component (CC) RNA polymerase II transcription factor complex 0.00000001918 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.004747 Highly Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0.02173InformativeInherited
Biological processVision0.0000006213Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0000001139Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.000009932Least InformativeDirect
Coding sequence diversityAlternative promoter usage0.000000001895Moderately InformativeDirect
DiseaseDisease mutation0.000593Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Molecular functionSteroid-binding0Highly InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000006285Moderately InformativeDirect
Post-translational modificationChromatin regulator0.000000009857InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.00001183Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationMethylation0.00000003441Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008946 SSF48508 Protein matches
Abstract


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 38 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Nuclear receptor ligand-binding domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 38 hidden Markov models representing the Nuclear receptor ligand-binding domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]