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MHC antigen-recognition domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   MHC antigen-recognition domain [ 54451]
Superfamily:   MHC antigen-recognition domain [ 54452]
Families:   MHC antigen-recognition domain [ 54453] (12)


Superfamily statistics
Genomes (93) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,661 96,097 190
Proteins 3,650 95,956 190


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 disease0.01635Least InformativeInherited
Disease Ontology (DO)organ system cancer0.0777Least InformativeInherited
Disease Ontology (DO)cardiovascular system disease0.2699Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.00000002106Moderately InformativeDirect
Disease Ontology (DO)disease by infectious agent0.0000003912Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.000001338Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.00001497Moderately InformativeDirect
Disease Ontology (DO)skin disease0.00002316Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.00002554Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.0001799Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.003331Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.006485Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.03828Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.04143Moderately InformativeInherited
Disease Ontology (DO)syndrome0.2875Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.713Moderately InformativeInherited
Disease Ontology (DO)multiple sclerosis0.0000000000006175InformativeDirect
Disease Ontology (DO)liver disease0.00000002104InformativeDirect
Disease Ontology (DO)alopecia0.0000344InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.00008086InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0003318InformativeDirect
Disease Ontology (DO)autosomal recessive disease0.0005313InformativeDirect
Disease Ontology (DO)allergic rhinitis0.0007541InformativeDirect
Disease Ontology (DO)peripheral nervous system disease0.007505InformativeInherited
Disease Ontology (DO)arthropathy0.00862InformativeInherited
Disease Ontology (DO)bullous skin disease0.01665InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.03045InformativeInherited
Disease Ontology (DO)myeloid leukemia0.09162InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)Graves' disease0.00000000005049Highly InformativeDirect
Disease Ontology (DO)Behcet's disease0.00000004822Highly InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0000001406Highly InformativeDirect
Disease Ontology (DO)sickle cell anemia0.00000192Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001992Highly InformativeDirect
Disease Ontology (DO)sarcoidosis0.00002801Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.00005994Highly InformativeDirect
Disease Ontology (DO)uveitis0.0001364Highly InformativeDirect
Disease Ontology (DO)metal metabolism disorder0.001066Highly InformativeInherited
Disease Ontology (DO)neuromuscular disease0.03282Highly InformativeInherited
Disease Ontology (DO)spondyloarthropathy0.4778Highly 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 system0.07773Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.09129Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1149Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1832Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.6441Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.6562Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.7599Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.02591Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thorax0.09114Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.2042Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.3471Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.3645Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.4265Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.4329Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.5002Moderately InformativeInherited
Phenotypic Abnormality (PA)CNS infection0.0002657InformativeDirect
Phenotypic Abnormality (PA)Edema0.0003277InformativeDirect
Phenotypic Abnormality (PA)Abnormal inflammatory response0.006518InformativeInherited
Phenotypic Abnormality (PA)Constitutional symptom0.03555InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.03808InformativeInherited
Phenotypic Abnormality (PA)Cognitive impairment0.04373InformativeInherited
Phenotypic Abnormality (PA)Abnormality of body weight0.1346InformativeInherited
Phenotypic Abnormality (PA)Functional respiratory abnormality0.3801InformativeInherited
Phenotypic Abnormality (PA)Abdominal symptom0.7477InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pleura0.00000237Highly InformativeDirect
Phenotypic Abnormality (PA)Pericarditis0.00001193Highly InformativeDirect
Phenotypic Abnormality (PA)Cough0.00007793Highly InformativeDirect
Phenotypic Abnormality (PA)Arthralgia0.00009172Highly InformativeDirect
Phenotypic Abnormality (PA)Pulmonary infiltrates0.0003006Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal sputum0.000302Highly InformativeDirect
Phenotypic Abnormality (PA)Abdominal pain0.0003417Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.0004619Highly InformativeDirect
Phenotypic Abnormality (PA)Weight loss0.0005205Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype0.0000002957Least InformativeDirect
Mammalian Phenotype (MP)abnormal leukocyte physiology0.000002729Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0006219Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.3196Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.4354Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.6996Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B lymphocyte antigen presentation0.0001339InformativeDirect
Mammalian Phenotype (MP)abnormal natural killer cell mediated cytotoxicity0.0003108InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.001044InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.00269InformativeInherited
Mammalian Phenotype (MP)abnormal effector T cell morphology0.1335InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell morphology0.2021InformativeInherited
Mammalian Phenotype (MP)decreased T cell number0.3777InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.8212InformativeInherited
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.0007679Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.0009993Highly InformativeDirect
Mammalian Phenotype (MP)abnormal CD8-positive, alpha beta T cell morphology0.1089Highly InformativeInherited
Mammalian Phenotype (MP)decreased alpha-beta T cell number0.2534Highly InformativeInherited

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)viscus0.2695Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pancreas0.0003993InformativeDirect

Document: XA annotation of SCOP domains

InterPro annotation
Cross references IPR011162 SSF54452 Protein matches
Abstract

This entry represents MHC class I and II-like antigen-recognition domains from:

  • MHC class II, N-terminal domains of alpha and beta chains [PubMed9768757]
  • MHC class I, alpha-1 and alpha-2 domains [PubMed15454423]
  • MHC class I related proteins, such as gammadelta T-cell ligand [PubMed17291278], Ulbp3 [PubMed12857997], Fc (IgG) receptor (alpha-1 and -2 domains) [PubMed7969498], CD1 (alpha-1 and -2 domains) [PubMed11677624], zinc-alpha-2-glycoprotein ZAG (fat depleting factor) [PubMed16475792]
  • Immunomodulatory protein m144, alpha-1 and alpha-2 domains [PubMed16500675]
  • Haemochromatosis protein Hfe, alpha-1 and alpha-2 domains [PubMed12667138]
  • NK cell ligand RAE-1 beta [PubMed12594837]
  • Endothelial protein C receptor (phospholipid-binding protein) [PubMed17327234]

More information about these proteins can be found at Protein of the Month: MHC.


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) · 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 92 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 MHC antigen-recognition 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 92 hidden Markov models representing the MHC antigen-recognition 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) · Xenopus Anatomy (XA) · Internal database links ]