SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


TNF-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   TNF-like [ 49841]
Superfamily:   TNF-like [ 49842]
Families:   TNF-like [ 49843] (14)


Superfamily statistics
Genomes (263) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 4,857 15,215 40
Proteins 4,643 14,867 40


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)cardiovascular system disease0.05603Least InformativeInherited
Disease Ontology (DO)nervous system disease0.1165Least InformativeInherited
Disease Ontology (DO)organ system cancer0.5603Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.0000000002669Moderately InformativeDirect
Disease Ontology (DO)artery disease0.00008911Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.000357Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.005607Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.007024Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.009505Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.02545Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2088Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.2813Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.4173Moderately InformativeInherited
Disease Ontology (DO)skin disease0.7788Moderately InformativeInherited
Disease Ontology (DO)atherosclerosis0.000001742InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.000001954InformativeDirect
Disease Ontology (DO)arthritis0.000002115InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.0000269InformativeDirect
Disease Ontology (DO)multiple sclerosis0.00005142InformativeDirect
Disease Ontology (DO)myocardial infarction0.0001962InformativeDirect
Disease Ontology (DO)intrinsic cardiomyopathy0.0003256InformativeDirect
Disease Ontology (DO)alopecia0.000548InformativeDirect
Disease Ontology (DO)bullous skin disease0.03607InformativeInherited
Disease Ontology (DO)pancreas disease0.05751InformativeInherited
Disease Ontology (DO)primary immunodeficiency disease0.09384InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1057InformativeInherited
Disease Ontology (DO)lymphoma0.13InformativeInherited
Disease Ontology (DO)rheumatic disease0.198InformativeInherited
Disease Ontology (DO)collagen disease0.2383InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.00000009325Highly InformativeDirect
Disease Ontology (DO)pemphigus0.000017Highly InformativeDirect
Disease Ontology (DO)primary open angle glaucoma0.00002645Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.00003278Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0002386Highly InformativeDirect
Disease Ontology (DO)Burkitt lymphoma0.0002924Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia0.0006403Highly InformativeDirect
Disease Ontology (DO)meningitis0.0008347Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.03974Highly 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 metabolism/homeostasis0.1779Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.3745Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.9401Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.002168Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system physiology0.2886Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.3531Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.4172Moderately InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.0008353InformativeDirect
Phenotypic Abnormality (PA)Abnormal cellular physiology0.0268InformativeInherited
Phenotypic Abnormality (PA)Abnormality of complement system0.05779InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal physiology0.09581InformativeInherited
Phenotypic Abnormality (PA)Glomerulonephritis0.000000795Highly InformativeDirect
Phenotypic Abnormality (PA)Increased antibody level in blood0.1572Highly 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 phenotype0.01535Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01819Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.01574Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.03799Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.04851Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.2016Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.3722Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.5985Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8965Moderately InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.000002842InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology0.00008395InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.0002204InformativeDirect
Mammalian Phenotype (MP)joint inflammation0.004136InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01128InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.01381InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.01711InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.01738InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02538InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.1785InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.2898InformativeInherited
Mammalian Phenotype (MP)abnormal IgG2a level0.0000005915Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.000005144Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology0.00003727Highly InformativeDirect
Mammalian Phenotype (MP)lymph node hypoplasia0.00004393Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.00007547Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0001129Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.000132Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal outer nuclear layer0.0006778Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus epithelium morphology0.0006997Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0007623Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response to transplant0.0008873Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.001711Highly InformativeInherited
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.01319Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3788Highly 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 IPR008983 SSF49842 Protein matches
Abstract

The tumour necrosis factor (TNF)-like domains are found in both TNF and C1q protein families. Structurally these domains self-associate to make a compact bell-shaped homotrimer, each monomer being composed of an anti-parallel beta-sheet sandwich with a jellyroll topology. Both TNF and C1q family members can be expressed as soluble plasma proteins or as type II membrane-bound proteins.

TNF family members bind extracellularly to cysteine-rich receptors, thereby inducing a clustering of the receptors, which subsequently triggers the intracellular apoptotic cascade. The TNF proteins are important mediators in inflammation, immune responses and cytotoxicity through their interaction with the TNF-R55 and the TNF-R75 cell-surface receptors [PubMed9442056]. Other TNF family members include the CD40 ligand (C-terminal TNF-like domain) which is involved in the immune response via the CD40 receptor [PubMed8589998], TRAIL which selectively induces apoptosis in tumour cells via DR4 and DR5 receptors [PubMed10651627], the RANK ligand which triggers osteoclastogenesis via the RANK receptor [PubMed11733492], and TALL-1 (soluble domain) which is involved in the immune response via the TACI, BCMA, and BAFF-R receptors [PubMed11862220].

C1q proteins also contain TNF-like domains. C1q family members include the serum protein ACRP30 (C-terminal TNF-like domain) which may be involved in energy homeostasis and obesity, and X-NC1 (C-terminal TNF-like domain) which is crucial for collagen X assembly in bone tissue [PubMed11839302].


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 39 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 TNF-like 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 39 hidden Markov models representing the TNF-like 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 ]