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4-helical cytokines superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   4-helical cytokines [ 47265]
Superfamily:   4-helical cytokines [ 47266] (3)
Families:   Long-chain cytokines [ 47267] (9)
  Short-chain cytokines [ 47286] (13)
  Interferons/interleukin-10 (IL-10) [ 47305] (8)


Superfamily statistics
Genomes (67) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 2,870 10,209 79
Proteins 2,850 10,150 77


Functional annotation
General category Processes_EC
Detailed category Immune response

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 cancer0.0001757Least InformativeDirect
Disease Ontology (DO)nervous system disease0.09196Least InformativeInherited
Disease Ontology (DO)skin disease0.000000001392Moderately InformativeDirect
Disease Ontology (DO)disease by infectious agent0.0000000152Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.00000007155Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.0000002197Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.0000126Moderately InformativeDirect
Disease Ontology (DO)syndrome0.0001267Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.0003716Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0004695Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.1071Moderately InformativeInherited
Disease Ontology (DO)disease of mental health0.1155Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.3548Moderately InformativeInherited
Disease Ontology (DO)lower respiratory tract disease0.4706Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.4816Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.8292Moderately InformativeInherited
Disease Ontology (DO)asthma0.00000000001742InformativeDirect
Disease Ontology (DO)periodontal disease0.0000000000365InformativeDirect
Disease Ontology (DO)multiple sclerosis0.00000003768InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0000001883InformativeDirect
Disease Ontology (DO)inflammatory bowel disease0.000000275InformativeDirect
Disease Ontology (DO)allergic rhinitis0.000002826InformativeDirect
Disease Ontology (DO)bullous pemphigoid0.00002736InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.0001056InformativeDirect
Disease Ontology (DO)muscle tissue disease0.0002112InformativeDirect
Disease Ontology (DO)arthropathy0.0004407InformativeDirect
Disease Ontology (DO)schizophrenia0.0347InformativeInherited
Disease Ontology (DO)developmental disorder of mental health0.09148InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.1367InformativeInherited
Disease Ontology (DO)lymphoma0.1572InformativeInherited
Disease Ontology (DO)collagen disease0.1668InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.2046InformativeInherited
Disease Ontology (DO)primary immunodeficiency disease0.2574InformativeInherited
Disease Ontology (DO)viral infectious disease0.3116InformativeInherited
Disease Ontology (DO)rheumatic disease0.3161InformativeInherited
Disease Ontology (DO)arthritis0.9004InformativeInherited
Disease Ontology (DO)parasitic protozoa infectious disease0.9609InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.0000000367Highly InformativeDirect
Disease Ontology (DO)celiac disease0.00000009002Highly InformativeDirect
Disease Ontology (DO)Chagas disease0.000001748Highly InformativeDirect
Disease Ontology (DO)opportunistic mycosis0.000004774Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.00004884Highly InformativeDirect
Disease Ontology (DO)otitis media0.0001184Highly InformativeDirect
Disease Ontology (DO)sarcoidosis0.0001462Highly InformativeDirect
Disease Ontology (DO)aggressive systemic mastocytosis0.0005086Highly InformativeDirect
Disease Ontology (DO)pertussis0.0007848Highly InformativeDirect
Disease Ontology (DO)eating disorder0.01504Highly InformativeInherited

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 cardiovascular system0.1022Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1215Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.4037Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.004114Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.08724Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.5914Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.6355Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.6882Moderately InformativeInherited
Phenotypic Abnormality (PA)Venous thrombosis0.0007028InformativeDirect
Phenotypic Abnormality (PA)Abnormal lung morphology0.005319InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral vasculature0.0136InformativeInherited
Phenotypic Abnormality (PA)Abnormal inflammatory response0.02269InformativeInherited
Phenotypic Abnormality (PA)Abnormal systemic arterial morphology0.04214InformativeInherited
Phenotypic Abnormality (PA)Edema0.04923InformativeInherited
Phenotypic Abnormality (PA)Abnormal ear morphology0.2137InformativeInherited
Phenotypic Abnormality (PA)Pericarditis0.00003261Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pleura0.009403Highly InformativeInherited
Phenotypic Abnormality (PA)Functional abnormality of the inner ear0.07852Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.000003756Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype0.00002694Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.237Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3092Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.3164Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.5824Least InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to infection0.0000000003305Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.000007221Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal leukocyte physiology0.0000141Moderately InformativeDirect
Mammalian Phenotype (MP)neoplasm0.0001028Moderately InformativeDirect
Mammalian Phenotype (MP)respiratory system phenotype0.0001318Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal protein level0.0001847Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.001522Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.002315Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.002977Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.006744Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.0105Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.03016Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.06701Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.08117Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.08465Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.09954Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.1327Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.1526Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.1681Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.3199Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4255Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.6346Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.8314Moderately InformativeInherited
Mammalian Phenotype (MP)increased susceptibility to infection0.0000000000143InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.000000005339InformativeDirect
Mammalian Phenotype (MP)abnormal circulating cytokine level0.00002105InformativeDirect
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.0001532InformativeDirect
Mammalian Phenotype (MP)abnormal liver physiology0.0001913InformativeDirect
Mammalian Phenotype (MP)abnormal natural killer cell mediated cytotoxicity0.0002795InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland morphology0.001098InformativeInherited
Mammalian Phenotype (MP)abnormal B lymphocyte antigen presentation0.002163InformativeInherited
Mammalian Phenotype (MP)abnormal intestine morphology0.008817InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.01756InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.03822InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.07441InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07506InformativeInherited
Mammalian Phenotype (MP)increased gland tumor incidence0.09566InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.1811InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.1967InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin level0.4486InformativeInherited
Mammalian Phenotype (MP)abnormal respiratory function0.5212InformativeInherited
Mammalian Phenotype (MP)abnormal response to transplant0.0000002813Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0000002989Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.000001149Highly InformativeDirect
Mammalian Phenotype (MP)increased circulating interleukin-17 level0.00000241Highly InformativeDirect
Mammalian Phenotype (MP)abnormal level of surface class II molecules0.000005642Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG2a level0.00001256Highly InformativeDirect
Mammalian Phenotype (MP)abnormal airway responsiveness0.00008398Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgE level0.0001246Highly InformativeDirect
Mammalian Phenotype (MP)abnormal susceptibility to weight loss0.0001927Highly InformativeDirect
Mammalian Phenotype (MP)abnormal glial cell physiology0.0003161Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland duct morphology0.0003858Highly InformativeDirect
Mammalian Phenotype (MP)increased gonad tumor incidence0.0004098Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.0005357Highly InformativeDirect
Mammalian Phenotype (MP)abnormal alveolar process morphology0.0007165Highly InformativeDirect
Mammalian Phenotype (MP)respiratory system inflammation0.0009979Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.001688Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovulation cycle0.04969Highly InformativeInherited
Mammalian Phenotype (MP)abnormal large intestine morphology0.1797Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to induced colitis0.2781Highly InformativeInherited

Document: MP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)cell0Least InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

InterPro annotation
Cross references IPR009079 SSF47266 Protein matches
Abstract

These domains display a core structure consisting of a closed bundle of four helices in a left-handed twist, with two crossover connections. Proteins containing such domains include long-chain cytokines, such as leukaemia inhibitory factor (LIF) [PubMed14511776], the growth hormone somatotropin [PubMed14507421], interleukin-6 [PubMed9118960] and leptin [PubMed9144295]; short-chain cytokines, such as erythropoietin [PubMed9783743], stem cell factor (SCF) [PubMed10880433], macrophage colony-stimulating factor (M-CSF) and interleukin-2, -3, -4, -5 and -13; and interferons/interleukin-10.


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) · 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 58 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 4-helical cytokines 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 58 hidden Markov models representing the 4-helical cytokines 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) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Internal database links ]