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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 2018_03 genome PDB chains (SCOP 1.75)
Domains 8,550 25,823 148
Proteins 8,431 25,490 148


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.02017Least InformativeInherited
Disease Ontology (DO)disease of metabolism0.0000001435Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001328Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.003355Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.003753Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.007071Moderately InformativeInherited
Disease Ontology (DO)overnutrition0.0000000394InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.00007107InformativeDirect
Disease Ontology (DO)alopecia0.0001667InformativeDirect
Disease Ontology (DO)viral infectious disease0.01352InformativeInherited
Disease Ontology (DO)physical disorder0.01549InformativeInherited
Disease Ontology (DO)urinary system cancer0.02395InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.07055InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.07142InformativeInherited
Disease Ontology (DO)breast cancer0.07207InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.07365InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.2618InformativeInherited
Disease Ontology (DO)pancreas disease0.7994InformativeInherited
Disease Ontology (DO)hypospadias0.000005032Highly InformativeDirect
Disease Ontology (DO)gallbladder disease0.0000667Highly InformativeDirect
Disease Ontology (DO)rubella0.0001033Highly InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001635Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.0007717Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.3604Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.9806Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.0033Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.2388Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.5624Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of circulating hormone level0.0001777InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pituitary gland0.002135InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.0242InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.05799InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.1608InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.4469InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.5965InformativeInherited
Phenotypic Abnormality (PA)Testicular gonadoblastoma0.00005428Highly InformativeDirect
Phenotypic Abnormality (PA)Hyperpituitarism0.00008832Highly InformativeDirect
Phenotypic Abnormality (PA)Primary amenorrhea0.0004812Highly InformativeDirect
Phenotypic Abnormality (PA)Polycystic ovaries0.0005339Highly InformativeDirect
Phenotypic Abnormality (PA)Infertility0.0006098Highly InformativeDirect
Phenotypic Abnormality (PA)Primary adrenal insufficiency0.1758Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.00001238Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00003089Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.00004016Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0002273Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.002382Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01056Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.0172Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.05383Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00000002467Moderately InformativeDirect
Mammalian Phenotype (MP)reproductive system phenotype0.0000001677Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000006265Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.0000007561Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.00000293Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.00005752Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.0005013Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal inflammatory response0.01006Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.01226Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01272Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.01699Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.02449Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.03046Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.06549Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.0843Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.118Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1584Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1911Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.2129Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.236Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.2925Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3189Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3897Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4113Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.4165Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.5245Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.5264Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.6325Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.000001491InformativeDirect
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00008121InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level0.00009217InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.0002429InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.0005573InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.00072InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.0008881InformativeDirect
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002593InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.002873InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0056InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.005662InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.006233InformativeInherited
Mammalian Phenotype (MP)abnormal renal corpuscle morphology0.006384InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.006829InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01484InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.01486InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.0174InformativeInherited
Mammalian Phenotype (MP)abnormal gland physiology0.02951InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.05058InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.05565InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.08997InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1223InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.1396InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.1539InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.1863InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2751InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3509InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.4268InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5368InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.5575InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level0.6256InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.6368InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6414InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.8017InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.8454InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9943InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level0.0000000009362Highly InformativeDirect
Mammalian Phenotype (MP)absent Harderian gland0.00000003123Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous0.00000006488Highly InformativeDirect
Mammalian Phenotype (MP)fused bronchial cartilage rings0.0000002613Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology0.0000003473Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0000005589Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight0.0000006405Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis0.00000077Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera0.000001769Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.000003171Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus0.000003429Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area0.00003988Highly InformativeDirect
Mammalian Phenotype (MP)decreased ventral retina size0.00006449Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0001046Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesonephros morphology0.0001132Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0002262Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.0003885Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.0004862Highly InformativeDirect
Mammalian Phenotype (MP)abnormal energy expenditure0.0005538Highly InformativeDirect
Mammalian Phenotype (MP)abnormal larynx morphology0.0006218Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0008322Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response/metabolism to endogenous compounds0.0008556Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.0009116Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cellular cholesterol metabolism0.00095Highly InformativeDirect
Mammalian Phenotype (MP)abnormal optic nerve morphology0.001547Highly InformativeInherited
Mammalian Phenotype (MP)abnormal renin activity0.001644Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.002187Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat pad morphology0.004094Highly InformativeInherited
Mammalian Phenotype (MP)abnormal intervertebral disk morphology0.01028Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian rhythm0.01902Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vas deferens morphology0.01924Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.02265Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.02484Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.04101Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.04399Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05014Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.05403Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06079Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.06759Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.08836Highly InformativeInherited
Mammalian Phenotype (MP)abnormal locomotor activation0.0936Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ureter morphology0.09765Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.1051Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1104Highly InformativeInherited
Mammalian Phenotype (MP)abnormal bone volume0.1493Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thyroid hormone level0.2122Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.2151Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2423Highly InformativeInherited
Mammalian Phenotype (MP)abnormal joint morphology0.2549Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.3452Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.3848Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.5775Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00003332Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant1Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant1Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.0000005897InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.0007549InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.201InformativeInherited
Worm Phenotype (WP)fat content increased0.000001777Highly InformativeDirect
Worm Phenotype (WP)hatching variant0.00005686Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.0000831Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.001998Highly InformativeInherited
Worm Phenotype (WP)social behavior variant0.01104Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.07633Least InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0.01758Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.03726Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.2061Least InformativeInherited
Fly Anatomy (FA)anatomical group0.2985Least InformativeInherited
Fly Anatomy (FA)nervous system0.5561Least InformativeInherited
Fly Anatomy (FA)somatic cell0.6026Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.0009138Moderately InformativeDirect
Fly Anatomy (FA)ganglion0.01408Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.0721Moderately InformativeInherited
Fly Anatomy (FA)neuron0.4033Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.4654Moderately InformativeInherited
Fly Anatomy (FA)head0.4802Moderately InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.0001261InformativeDirect
Fly Anatomy (FA)interneuron0.0007439InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion0.03172InformativeInherited
Fly Anatomy (FA)neuromere0.03865InformativeInherited
Fly Anatomy (FA)adult brain0.04973InformativeInherited
Fly Anatomy (FA)mushroom body intrinsic neuron0.000001275Highly InformativeDirect
Fly Anatomy (FA)adult MBp lineage neuron0.000001275Highly InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion neuron0.00001625Highly InformativeDirect
Fly Anatomy (FA)mushroom body medial lobe0.007973Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0.9119Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.3785Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.8092Moderately InformativeInherited
Xenopus ANatomical entity (XAN)foregut0.0005124Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.1041Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)tailbud stage0.8707InformativeInherited

Document: XA 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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) ]

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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Internal database links ]