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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 cancer0.0001773Least InformativeDirect
Disease Ontology (DO)nervous system disease0.09157Least InformativeInherited
Disease Ontology (DO)skin disease0.000000001415Moderately InformativeDirect
Disease Ontology (DO)disease by infectious agent0.00000001577Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.00000007246Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.0000002221Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.00001272Moderately InformativeDirect
Disease Ontology (DO)syndrome0.0001276Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.0003746Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.000486Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.1096Moderately InformativeInherited
Disease Ontology (DO)disease of mental health0.1155Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.3543Moderately InformativeInherited
Disease Ontology (DO)lower respiratory tract disease0.4705Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.4825Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.8285Moderately InformativeInherited
Disease Ontology (DO)asthma0.00000000001772InformativeDirect
Disease Ontology (DO)periodontal disease0.00000000003717InformativeDirect
Disease Ontology (DO)multiple sclerosis0.00000003822InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.000000191InformativeDirect
Disease Ontology (DO)inflammatory bowel disease0.0000002789InformativeDirect
Disease Ontology (DO)allergic rhinitis0.000002859InformativeDirect
Disease Ontology (DO)bullous pemphigoid0.00002766InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.0001068InformativeDirect
Disease Ontology (DO)muscle tissue disease0.0002065InformativeDirect
Disease Ontology (DO)arthropathy0.0004847InformativeDirect
Disease Ontology (DO)schizophrenia0.0348InformativeInherited
Disease Ontology (DO)developmental disorder of mental health0.09171InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.137InformativeInherited
Disease Ontology (DO)lymphoma0.1576InformativeInherited
Disease Ontology (DO)collagen disease0.1667InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.2079InformativeInherited
Disease Ontology (DO)primary immunodeficiency disease0.2577InformativeInherited
Disease Ontology (DO)viral infectious disease0.313InformativeInherited
Disease Ontology (DO)rheumatic disease0.3165InformativeInherited
Disease Ontology (DO)arthritis0.8915InformativeInherited
Disease Ontology (DO)parasitic protozoa infectious disease0.9602InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.00000003721Highly InformativeDirect
Disease Ontology (DO)celiac disease0.00000009134Highly InformativeDirect
Disease Ontology (DO)Chagas disease0.000001772Highly InformativeDirect
Disease Ontology (DO)opportunistic mycosis0.000004845Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.00004943Highly InformativeDirect
Disease Ontology (DO)otitis media0.0001197Highly InformativeDirect
Disease Ontology (DO)sarcoidosis0.0001477Highly InformativeDirect
Disease Ontology (DO)aggressive systemic mastocytosis0.0005129Highly InformativeDirect
Disease Ontology (DO)pertussis0.0007914Highly InformativeDirect
Disease Ontology (DO)eating disorder0.01512Highly 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 system0.1128Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.2128Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.05911Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.3442Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.6136Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.7664Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal thrombosis0.0136InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.01429InformativeInherited
Phenotypic Abnormality (PA)Edema0.07297InformativeInherited
Phenotypic Abnormality (PA)Pericarditis0.00005609Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pleura0.00917Highly 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 phenotype0.000003727Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype0.00002695Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.2365Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.3091Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body region phenotype0.3165Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.5832Least InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.000007194Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal leukocyte physiology0.00001404Moderately InformativeDirect
Mammalian Phenotype (MP)neoplasm0.0001026Moderately InformativeDirect
Mammalian Phenotype (MP)respiratory system phenotype0.0001312Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal protein level0.0001857Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.00153Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.002295Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.002945Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.006803Moderately InformativeInherited
Mammalian Phenotype (MP)reproductive system phenotype0.01047Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.02976Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.06705Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.0809Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.08463Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.09955Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.1328Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.1529Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.1681Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.3212Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4258Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.6331Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.8314Moderately InformativeInherited
Mammalian Phenotype (MP)increased susceptibility to infection0.00000000001422InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.000000005318InformativeDirect
Mammalian Phenotype (MP)abnormal circulating cytokine level0.00002198InformativeDirect
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.0001536InformativeDirect
Mammalian Phenotype (MP)abnormal liver physiology0.0001911InformativeDirect
Mammalian Phenotype (MP)abnormal natural killer cell mediated cytotoxicity0.0002798InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland morphology0.001081InformativeInherited
Mammalian Phenotype (MP)abnormal B lymphocyte antigen presentation0.002174InformativeInherited
Mammalian Phenotype (MP)abnormal intestine morphology0.008823InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.01758InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.03761InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.07447InformativeInherited
Mammalian Phenotype (MP)abnormal viscerocranium morphology0.07499InformativeInherited
Mammalian Phenotype (MP)increased gland tumor incidence0.09586InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.181InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.1974InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin level0.4433InformativeInherited
Mammalian Phenotype (MP)abnormal respiratory function0.5213InformativeInherited
Mammalian Phenotype (MP)abnormal response to transplant0.0000002811Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0000002996Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.000001149Highly InformativeDirect
Mammalian Phenotype (MP)increased circulating interleukin-17 level0.000002415Highly InformativeDirect
Mammalian Phenotype (MP)abnormal level of surface class II molecules0.000005645Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG2a level0.00001256Highly InformativeDirect
Mammalian Phenotype (MP)abnormal airway responsiveness0.00008405Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgE level0.0001272Highly InformativeDirect
Mammalian Phenotype (MP)abnormal susceptibility to weight loss0.0001924Highly InformativeDirect
Mammalian Phenotype (MP)abnormal glial cell physiology0.0003163Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland duct morphology0.0003857Highly InformativeDirect
Mammalian Phenotype (MP)increased gonad tumor incidence0.0004096Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.0005355Highly InformativeDirect
Mammalian Phenotype (MP)abnormal alveolar process morphology0.0007168Highly InformativeDirect
Mammalian Phenotype (MP)respiratory system inflammation0.0009966Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.001685Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ovulation cycle0.04973Highly InformativeInherited
Mammalian Phenotype (MP)abnormal large intestine morphology0.1798Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to induced colitis0.2781Highly InformativeInherited

Document: MP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) 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 ]