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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)nervous system disease0.1158Least InformativeInherited
Disease Ontology (DO)organ system cancer0.561Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.0000000002669Moderately InformativeDirect
Disease Ontology (DO)artery disease0.00008903Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0003573Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.005612Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.007035Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.009512Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.02547Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2092Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.2812Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.4165Moderately InformativeInherited
Disease Ontology (DO)skin disease0.7788Moderately InformativeInherited
Disease Ontology (DO)atherosclerosis0.000001742InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.000001954InformativeDirect
Disease Ontology (DO)arthritis0.000002116InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.00002687InformativeDirect
Disease Ontology (DO)multiple sclerosis0.00005148InformativeDirect
Disease Ontology (DO)myocardial infarction0.0001962InformativeDirect
Disease Ontology (DO)intrinsic cardiomyopathy0.000313InformativeDirect
Disease Ontology (DO)alopecia0.0005481InformativeDirect
Disease Ontology (DO)bullous skin disease0.03607InformativeInherited
Disease Ontology (DO)pancreas disease0.05749InformativeInherited
Disease Ontology (DO)primary immunodeficiency disease0.09383InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1057InformativeInherited
Disease Ontology (DO)lymphoma0.1299InformativeInherited
Disease Ontology (DO)rheumatic disease0.198InformativeInherited
Disease Ontology (DO)collagen disease0.2384InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.00000009326Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001702Highly InformativeDirect
Disease Ontology (DO)primary open angle glaucoma0.00002639Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.00003282Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0002388Highly InformativeDirect
Disease Ontology (DO)Burkitt lymphoma0.0002926Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia0.0006413Highly InformativeDirect
Disease Ontology (DO)meningitis0.0008367Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.03977Highly 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/homeostasis0.1358Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.3049Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.9746Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.001194Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.2998Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system physiology0.3417Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.4826Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of B cell physiology0.0008869InformativeDirect
Phenotypic Abnormality (PA)Abnormality of complement system0.07746InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal physiology0.1245InformativeInherited
Phenotypic Abnormality (PA)Abnormal renal morphology0.2696InformativeInherited
Phenotypic Abnormality (PA)Glomerulonephritis0.000001559Highly InformativeDirect
Phenotypic Abnormality (PA)Autoimmunity0.002448Highly InformativeInherited
Phenotypic Abnormality (PA)Abnormal immunoglobulin level0.9487Highly 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 phenotype0.01541Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01827Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.01554Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.03797Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.04806Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.2001Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.3721Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.5986Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8963Moderately InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.000002848InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology0.00008396InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.0002229InformativeDirect
Mammalian Phenotype (MP)joint inflammation0.004123InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01114InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.01381InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.01688InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.01738InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02533InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.1786InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.2891InformativeInherited
Mammalian Phenotype (MP)abnormal IgG2a level0.0000005926Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.000005149Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology0.00003545Highly InformativeDirect
Mammalian Phenotype (MP)lymph node hypoplasia0.00004394Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.00007549Highly 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 layer0.0006758Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus epithelium morphology0.0006975Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0007603Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response to transplant0.000884Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.001704Highly InformativeInherited
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.01319Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3787Highly 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 ]