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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 2017_06 genome PDB chains (SCOP 1.75)
Domains 3,661 88,764 190
Proteins 3,650 88,637 190


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 stimulus0.17330Least InformativeInherited
Biological Process (BP)immune system process0.000072150Moderately InformativeDirect
Biological Process (BP)immune response0.00027930InformativeDirect
Cellular Component (CC)membrane0.00087670Least InformativeDirect
Cellular Component (CC)plasma membrane0.03150Moderately InformativeInherited

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) biological regulation 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) defense response 0 Moderately Informative Direct
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) response to organic substance 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.0001983 Moderately Informative Direct
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0002622 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.0002764 Moderately Informative Direct
Biological Process (BP) protein complex biogenesis 0.0000001124 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0 Moderately Informative Direct
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.00463 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.03942 Moderately Informative Inherited
Biological Process (BP) cell activation 0.000000000001347 Informative Direct
Biological Process (BP) regulation of cytokine production 0.000000000008936 Informative Direct
Biological Process (BP) positive regulation of immune system process 0 Informative Direct
Biological Process (BP) immune response 0 Informative Direct
Biological Process (BP) cell surface receptor signaling pathway 0 Informative Direct
Biological Process (BP) response to bacterium 0.000001477 Informative Direct
Biological Process (BP) regulation of hormone levels 0.0000005033 Informative Direct
Biological Process (BP) regulation of defense response 0 Informative Direct
Biological Process (BP) regulation of protein localization 0.00004952 Informative Direct
Biological Process (BP) regulation of immune response 0 Informative Direct
Biological Process (BP) regulation of secretion 0.000003775 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.0005394 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.00008266 Informative Direct
Biological Process (BP) regulation of cellular localization 0.00004428 Informative Direct
Biological Process (BP) regulation of peptide transport 0.000004099 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.1643 Informative Inherited
Biological Process (BP) protein oligomerization 0.07636 Informative Inherited
Biological Process (BP) regulation of nervous system development 1 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1483 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.1668 Informative Inherited
Biological Process (BP) immune effector process 1 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.6455 Informative Inherited
Biological Process (BP) secretion by cell 0.1802 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.003403 Informative Inherited
Biological Process (BP) generation of neurons 0.7946 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.3234 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.4037 Informative Inherited
Biological Process (BP) cellular protein complex assembly 0.552 Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.0008749 Highly Informative Direct
Biological Process (BP) neutrophil mediated immunity 0.0004914 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.00000002257 Highly Informative Direct
Biological Process (BP) positive regulation of immune effector process 0.0000000007767 Highly Informative Direct
Biological Process (BP) regulation of leukocyte mediated immunity 0 Highly Informative Direct
Biological Process (BP) immune response-activating signal transduction 0.0005079 Highly Informative Direct
Biological Process (BP) positive regulation of peptide secretion 0.000000000003529 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response based on somatic recombination of immune receptors b 0.00002883 Highly Informative Direct
Biological Process (BP) protein folding 0.000000000000007296 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.0000001083 Highly Informative Direct
Biological Process (BP) negative regulation of cell development 0.000005871 Highly Informative Direct
Biological Process (BP) regulation of neuron projection development 0.0003557 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of cell killing 0 Highly Informative Direct
Biological Process (BP) negative regulation of defense response 0.000000009924 Highly Informative Direct
Biological Process (BP) positive regulation of homeostatic process 0.0000001744 Highly Informative Direct
Biological Process (BP) granulocyte activation 0.0006192 Highly Informative Direct
Biological Process (BP) innate immune response 0 Highly Informative Direct
Biological Process (BP) positive regulation of cell adhesion 0 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 0.00000000005408 Highly Informative Direct
Biological Process (BP) positive regulation of protein transport 0.0000003224 Highly Informative Direct
Biological Process (BP) regulation of reactive oxygen species biosynthetic process 0 Highly Informative Direct
Biological Process (BP) positive regulation of secretion by cell 0.000001246 Highly Informative Direct
Biological Process (BP) positive regulation of reactive oxygen species metabolic process 0.00000000000004736 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 0.008839 Highly Informative Inherited
Biological Process (BP) regulation of hemopoiesis 0.4468 Highly Informative Inherited
Biological Process (BP) regulation of lymphocyte proliferation 1 Highly Informative Inherited
Biological Process (BP) leukocyte degranulation 1 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 0.009351 Highly Informative Inherited
Biological Process (BP) negative regulation of cytokine production 0.005453 Highly Informative Inherited
Biological Process (BP) positive regulation of lymphocyte activation 0.09334 Highly Informative Inherited
Biological Process (BP) lymphocyte activation 0.02568 Highly Informative Inherited
Biological Process (BP) negative regulation of nervous system development 0.0109 Highly Informative Inherited
Biological Process (BP) inflammatory response 1 Highly Informative Inherited
Biological Process (BP) myeloid cell activation involved in immune response 0.6025 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) receptor binding 0.000002186 Informative Direct
Molecular Function (MF) amide binding 0 Informative Direct
Molecular Function (MF) macromolecular complex binding 0.3725 Informative Inherited
Molecular Function (MF) signal transducer activity 0.02267 Informative Inherited
Molecular Function (MF) molecular transducer activity 0.0032 Informative Inherited
Molecular Function (MF) transmembrane signaling receptor activity 0.00002787 Highly Informative Direct
Molecular Function (MF) peptide binding 0 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000000004425 Least Informative Direct
Cellular Component (CC) protein complex 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) vacuole 0 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0 Moderately Informative Direct
Cellular Component (CC) intrinsic component of membrane 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0 Moderately Informative Direct
Cellular Component (CC) bounding membrane of organelle 0 Moderately Informative Direct
Cellular Component (CC) membrane protein complex 0 Moderately Informative Direct
Cellular Component (CC) whole membrane 0 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.005914 Moderately Informative Inherited
Cellular Component (CC) lytic vacuole 0 Informative Direct
Cellular Component (CC) extracellular space 0.00003601 Informative Direct
Cellular Component (CC) endosome 0 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0 Informative Direct
Cellular Component (CC) Golgi apparatus 0 Informative Direct
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular organelle 0.0003953 Informative Direct
Cellular Component (CC) cytoplasmic vesicle part 0 Informative Direct
Cellular Component (CC) vacuolar part 0 Informative Direct
Cellular Component (CC) side of membrane 0 Informative Direct
Cellular Component (CC) plasma membrane protein complex 0 Informative Direct
Cellular Component (CC) lysosomal membrane 0.000000000000004535 Highly Informative Direct
Cellular Component (CC) late endosome 0.00007421 Highly Informative Direct
Cellular Component (CC) Golgi-associated vesicle 0 Highly Informative Direct
Cellular Component (CC) external side of plasma membrane 0 Highly Informative Direct
Cellular Component (CC) endosome membrane 0 Highly Informative Direct
Cellular Component (CC) coated vesicle 0 Highly Informative Direct
Cellular Component (CC) endocytic vesicle 0 Highly Informative Direct
Cellular Component (CC) integral component of endoplasmic reticulum membrane 0 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.0000000000000228 Highly Informative Direct
Cellular Component (CC) extracellular exosome 0.0001269 Highly Informative Direct
Cellular Component (CC) Golgi subcompartment 0 Highly Informative Direct
Cellular Component (CC) anchored component of membrane 0.06035 Highly Informative Inherited
Cellular Component (CC) intrinsic component of plasma membrane 1 Highly Informative Inherited

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processHost-virus interaction0Moderately InformativeDirect
Biological processImmunity0Moderately InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentEndoplasmic reticulum0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentGolgi apparatus0.00000000000009385Moderately InformativeDirect
Cellular componentLysosome0InformativeDirect
Cellular componentGPI-anchor0.0002454InformativeDirect
Coding sequence diversityPolymorphism0Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
DomainImmunoglobulin domain0InformativeDirect
Molecular functionIron1Moderately InformativeInherited
Molecular functionIron transport0.0000000005063Highly 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 · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · 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) · UniProtKB KeyWords (KW) · Internal database links ]