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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 0 190
Proteins 3,650 0 190


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 disease0.01632Least InformativeInherited
Disease Ontology (DO)organ system cancer0.07751Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.00000002071Moderately InformativeDirect
Disease Ontology (DO)disease by infectious agent0.0000003815Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.000001321Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.00001483Moderately InformativeDirect
Disease Ontology (DO)skin disease0.0000229Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.00002527Moderately InformativeDirect
Disease Ontology (DO)gastrointestinal system disease0.0001789Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.003311Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.006471Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.03816Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.04125Moderately InformativeInherited
Disease Ontology (DO)syndrome0.2874Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.7135Moderately InformativeInherited
Disease Ontology (DO)multiple sclerosis0.0000000000006095InformativeDirect
Disease Ontology (DO)liver disease0.00000002069InformativeDirect
Disease Ontology (DO)alopecia0.000034InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.00008007InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0003289InformativeDirect
Disease Ontology (DO)autosomal recessive disease0.0005264InformativeDirect
Disease Ontology (DO)allergic rhinitis0.0007475InformativeDirect
Disease Ontology (DO)peripheral nervous system disease0.007461InformativeInherited
Disease Ontology (DO)arthropathy0.008084InformativeInherited
Disease Ontology (DO)bullous skin disease0.01658InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.03029InformativeInherited
Disease Ontology (DO)myeloid leukemia0.09132InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)Graves' disease0.00000000004954Highly InformativeDirect
Disease Ontology (DO)Behcet's disease0.00000004748Highly InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0000001385Highly InformativeDirect
Disease Ontology (DO)sickle cell anemia0.000001891Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001968Highly InformativeDirect
Disease Ontology (DO)sarcoidosis0.0000277Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.00005922Highly InformativeDirect
Disease Ontology (DO)uveitis0.0001351Highly InformativeDirect
Disease Ontology (DO)metal metabolism disorder0.001054Highly InformativeInherited
Disease Ontology (DO)neuromuscular disease0.03268Highly InformativeInherited
Disease Ontology (DO)spondyloarthropathy0.4727Highly 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 system0.07775Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.08893Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.1144Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.1673Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.6679Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.6687Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0.7293Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of digestive system physiology0.02359Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.1985Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.292Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.3497Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal eye physiology0.3967Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.4295Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system morphology0.4801Moderately InformativeInherited
Phenotypic Abnormality (PA)Edema0.0002622InformativeDirect
Phenotypic Abnormality (PA)CNS infection0.0002966InformativeDirect
Phenotypic Abnormality (PA)Constitutional symptom0.03067InformativeInherited
Phenotypic Abnormality (PA)Abnormal lung morphology0.03869InformativeInherited
Phenotypic Abnormality (PA)Cognitive impairment0.04084InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the thorax0.08832InformativeInherited
Phenotypic Abnormality (PA)Abnormality of body weight0.1317InformativeInherited
Phenotypic Abnormality (PA)Functional respiratory abnormality0.3513InformativeInherited
Phenotypic Abnormality (PA)Abdominal symptom0.742InformativeInherited
Phenotypic Abnormality (PA)Increased inflammatory response1InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the pleura0.000002531Highly InformativeDirect
Phenotypic Abnormality (PA)Pericarditis0.00001336Highly InformativeDirect
Phenotypic Abnormality (PA)Cough0.00006198Highly InformativeDirect
Phenotypic Abnormality (PA)Arthralgia0.0001116Highly InformativeDirect
Phenotypic Abnormality (PA)Pulmonary infiltrates0.000292Highly InformativeDirect
Phenotypic Abnormality (PA)Abdominal pain0.0003465Highly InformativeDirect
Phenotypic Abnormality (PA)Memory impairment0.0003846Highly InformativeDirect
Phenotypic Abnormality (PA)Weight loss0.0004579Highly InformativeDirect
Phenotypic Abnormality (PA)Hemoptysis0.0006215Highly 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 phenotype0.000000297Least InformativeDirect
Mammalian Phenotype (MP)abnormal leukocyte physiology0.000002735Moderately InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to infection0.0003316Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0006228Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.3195Moderately 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 presentation0.000134InformativeDirect
Mammalian Phenotype (MP)abnormal natural killer cell mediated cytotoxicity0.000311InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.001046InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.002692InformativeInherited
Mammalian Phenotype (MP)abnormal effector T cell morphology0.1335InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell morphology0.2022InformativeInherited
Mammalian Phenotype (MP)decreased T cell number0.3776InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.8212InformativeInherited
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.0007684Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.0009997Highly 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)viscus0.2694Moderately InformativeInherited
Xenopus ANatomical entity (XAN)pancreas0.0003953InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processImmunity0Moderately InformativeDirect
Biological processHost-virus interaction0Moderately InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus0.00000000000009648Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect
Cellular componentGPI-anchor0.0002345InformativeDirect
Coding sequence diversityPolymorphism0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Molecular functionIron1Moderately InformativeInherited
Molecular functionIron transport0.0000000004899Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect

Document: KW 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) · UniProtKB KeyWords (KW) ]

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 72 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 72 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) · UniProtKB KeyWords (KW) · Internal database links ]