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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 2014_06 PDB chains (SCOP 1.75)
Domains 3,661 62,409 190
Proteins 3,650 62,349 190


Functional annotation
General category Processes_EC
Detailed category Immune response

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)response to stimulus0.15390Least InformativeInherited
Biological Process (BP)developmental process0.00057641Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0016751Least InformativeInherited
Biological Process (BP)immune system process00Moderately InformativeDirect
Biological Process (BP)organ development0.0000057170.00004345Moderately InformativeDirect
Biological Process (BP)positive regulation of response to stimulus0.000089630Moderately InformativeDirect
Biological Process (BP)multi-organism process0.013360.00000000000002112Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.0004911Moderately InformativeInherited
Biological Process (BP)regulation of immune effector process00.000000002975InformativeDirect
Biological Process (BP)regulation of immune response0.000000000001350InformativeDirect
Biological Process (BP)sensory organ development0.0000000000079120InformativeDirect
Biological Process (BP)positive regulation of immune system process0.00000052910InformativeDirect
Biological Process (BP)defense response0.00053360InformativeDirect
Biological Process (BP)response to other organism0.0019950.000000000001293InformativeInherited
Biological Process (BP)ear development00Highly InformativeDirect
Biological Process (BP)positive regulation of cell killing00Highly InformativeDirect
Biological Process (BP)positive regulation of adaptive immune response00Highly InformativeDirect
Biological Process (BP)regulation of leukocyte mediated cytotoxicity00Highly InformativeDirect
Biological Process (BP)regulation of adaptive immune response based on somatic recombination of immune receptors built from00Highly InformativeDirect
Biological Process (BP)regulation of lymphocyte mediated immunity00Highly InformativeDirect
Biological Process (BP)antigen processing and presentation0.0000000000035050Highly InformativeDirect
Biological Process (BP)positive regulation of leukocyte mediated immunity0.0016870Highly InformativeInherited
Molecular Function (MF)binding0.0085450Least InformativeInherited
Molecular Function (MF)amide binding0.0000029840InformativeDirect
Molecular Function (MF)peptide binding0.00000020980Highly InformativeDirect
Molecular Function (MF)antigen binding0.00002870Highly InformativeDirect
Cellular Component (CC)membrane0.00004610Least InformativeDirect
Cellular Component (CC)plasma membrane0.00070040Moderately InformativeDirect
Cellular Component (CC)cell surface0.000000014330InformativeDirect
Cellular Component (CC)external side of plasma membrane0.00080350Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) protein metabolic process 0.1357 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.3747 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) organ development 0.00004345 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.00000000000002112 Moderately Informative Direct
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) response to organic substance 0 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0000005251 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0008044 Moderately Informative Direct
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.02335 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of immune effector process 0.000000002975 Informative Direct
Biological Process (BP) regulation of immune response 0 Informative Direct
Biological Process (BP) sensory organ development 0 Informative Direct
Biological Process (BP) positive regulation of immune system process 0 Informative Direct
Biological Process (BP) defense response 0 Informative Direct
Biological Process (BP) response to other organism 0.000000000001293 Informative Direct
Biological Process (BP) immune response 0 Informative Direct
Biological Process (BP) response to cytokine stimulus 0 Informative Direct
Biological Process (BP) regulation of cytokine production 0.000000000000003741 Informative Direct
Biological Process (BP) regulation of defense response 0.00000000000002112 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 0.00001377 Informative Direct
Biological Process (BP) regulation of secretion 0.0001863 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0001916 Informative Direct
Biological Process (BP) protein oligomerization 0.1907 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.4978 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.06318 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.131 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.7863 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1 Informative Inherited
Biological Process (BP) positive regulation of transport 0.8934 Informative Inherited
Biological Process (BP) leukocyte activation 1 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.3228 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) immune effector process 1 Informative Inherited
Biological Process (BP) response to wounding 1 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 1 Informative Inherited
Biological Process (BP) ear development 0 Highly Informative Direct
Biological Process (BP) positive regulation of cell killing 0 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0 Highly Informative Direct
Biological Process (BP) regulation of leukocyte mediated cytotoxicity 0 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 0 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 0 Highly Informative Direct
Biological Process (BP) antigen processing and presentation 0 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte mediated immunity 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of nitric oxide biosynthetic process 0 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0 Highly Informative Direct
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) protein tetramerization 0.000000000000007318 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 0.00000000007226 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0000000001504 Highly Informative Direct
Biological Process (BP) negative regulation of cell activation 0.000000000411 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 0.000000000497 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.0000007973 Highly Informative Direct
Biological Process (BP) immune response-regulating cell surface receptor signaling pathway 0.000001225 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.000002483 Highly Informative Direct
Biological Process (BP) innate immune response 0.000005541 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 0.000008314 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.00001802 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.00002857 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 0.07008 Highly Informative Inherited
Biological Process (BP) immune response-activating signal transduction 0.003979 Highly Informative Inherited
Biological Process (BP) T cell differentiation 0.06176 Highly Informative Inherited
Biological Process (BP) positive regulation of defense response 0.7285 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.001631 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 0.004537 Highly Informative Inherited
Biological Process (BP) regulation of innate immune response 1 Highly Informative Inherited
Biological Process (BP) inflammatory response 1 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) receptor binding 0.0001268 Informative Direct
Molecular Function (MF) lipid binding 0.9557 Informative Inherited
Molecular Function (MF) receptor activity 0.01042 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.05159 Informative Inherited
Molecular Function (MF) peptide binding 0 Highly Informative Direct
Molecular Function (MF) antigen binding 0 Highly Informative Direct
Molecular Function (MF) protein complex binding 0.4661 Highly Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00000001337 Least Informative Direct
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.00000003743 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0 Moderately Informative Direct
Cellular Component (CC) organelle membrane 0 Moderately Informative Direct
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) vacuolar part 0 Informative Direct
Cellular Component (CC) coated vesicle 0 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0 Informative Direct
Cellular Component (CC) lytic vacuole 0 Informative Direct
Cellular Component (CC) integral to membrane 0.7023 Informative Inherited
Cellular Component (CC) intrinsic to plasma membrane 1 Informative Inherited
Cellular Component (CC) external side of plasma membrane 0 Highly Informative Direct
Cellular Component (CC) transport vesicle 0 Highly Informative Direct
Cellular Component (CC) intrinsic to organelle membrane 0 Highly Informative Direct
Cellular Component (CC) endosomal part 0 Highly Informative Direct
Cellular Component (CC) endocytic vesicle 0 Highly Informative Direct
Cellular Component (CC) lysosome 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 0.000000000000006075 Highly Informative Direct
Cellular Component (CC) late endosome 0.00000000003007 Highly Informative Direct
Cellular Component (CC) anchored to membrane 0.1679 Highly Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease0.000002481Least InformativeDirect
Disease Ontology (DO)nervous system disease0.03163Least InformativeInherited
Disease Ontology (DO)organ system cancer0.08884Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.00000002533Moderately InformativeDirect
Disease Ontology (DO)neurodegenerative disease0.000004656Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.00000617Moderately InformativeDirect
Disease Ontology (DO)skin disease0.00003902Moderately InformativeDirect
Disease Ontology (DO)connective tissue disease0.0001275Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.0002519Moderately InformativeDirect
Disease Ontology (DO)leukemia0.0009489Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.00659Moderately InformativeInherited
Disease Ontology (DO)genetic disease0.01601Moderately InformativeInherited
Disease Ontology (DO)bacterial infectious disease0.1066Moderately InformativeInherited
Disease Ontology (DO)syndrome0.1936Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.5315Moderately InformativeInherited
Disease Ontology (DO)multiple sclerosis0.000000000001958InformativeDirect
Disease Ontology (DO)liver disease0.00000003469InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0000000703InformativeDirect
Disease Ontology (DO)alopecia0.00002925InformativeDirect
Disease Ontology (DO)primary bacterial infectious disease0.0002957InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.0003396InformativeDirect
Disease Ontology (DO)allergic rhinitis0.0004905InformativeDirect
Disease Ontology (DO)thyroid gland disease0.00307InformativeInherited
Disease Ontology (DO)arthropathy0.003811InformativeInherited
Disease Ontology (DO)autosomal recessive disease0.02014InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type IV disease0.02458InformativeInherited
Disease Ontology (DO)neuropathy0.02963InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)Graves' disease0.0000000006723Highly InformativeDirect
Disease Ontology (DO)Behcet's disease0.00000001973Highly InformativeDirect
Disease Ontology (DO)sickle cell anemia0.0000008926Highly InformativeDirect
Disease Ontology (DO)spondylitis0.000006353Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001139Highly InformativeDirect
Disease Ontology (DO)sarcoidosis0.00001593Highly InformativeDirect
Disease Ontology (DO)intrahepatic cholestasis0.00005659Highly InformativeDirect
Disease Ontology (DO)rheumatic fever0.0002071Highly InformativeDirect
Disease Ontology (DO)leprosy0.0004347Highly InformativeDirect
Disease Ontology (DO)metal metabolism disorder0.001625Highly InformativeInherited
Disease Ontology (DO)neuromuscular disease0.04066Highly 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 nervous system physiology0.4496Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of higher mental function0.07624Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cardiovascular system physiology0.02387InformativeInherited
Phenotypic Abnormality (PA)Arrhythmia0.002592Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)hematopoietic system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology0.000008989Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.00001562Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune cell physiology0.07436Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.07826Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.08742Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.1199Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.1841Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology0.0000008179InformativeDirect
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.000002685InformativeDirect
Mammalian Phenotype (MP)abnormal antigen presentation0.000008287InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.0002338InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.06181InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.3475InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.5384InformativeInherited
Mammalian Phenotype (MP)decreased leukocyte cell number0.6154InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.00006948Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cytotoxic T cell physiology0.0007266Highly InformativeDirect
Mammalian Phenotype (MP)abnormal alpha-beta T cell number0.2319Highly InformativeInherited
Mammalian Phenotype (MP)decreased T cell number0.2906Highly InformativeInherited

Document: MP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)alimentary system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0Least InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentEndoplasmic reticulum6.428e-16Moderately InformativeDirect
Cellular componentGolgi apparatus0.000000000000026Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect
Cellular componentGPI-anchor0.0007471InformativeDirect
Coding sequence diversityPolymorphism0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]