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Conserved domains on  [gi|18765715|ref|NP_006111|]
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HLA class II histocompatibility antigen, DM alpha chain precursor [Homo sapiens]

Protein Classification

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List of domain hits

Name Accession Description Interval E-value
IgC1_MHC_II_alpha_HLA-DM cd21009
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
125-218 1.93e-65

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DM. Human HLA-DM, also known as H2-M in mice, plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


:

Pssm-ID: 409600  Cd Length: 94  Bit Score: 198.73  E-value: 1.93e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 125 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIV 204
Cdd:cd21009   1 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQLHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIV 80
                        90
                ....*....|....
gi 18765715 205 THEIDRYTAIAYWV 218
Cdd:cd21009  81 THEIDRYTAIAYWV 94
MHC_II_alpha smart00920
Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on ...
41-123 2.41e-31

Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


:

Pssm-ID: 214913  Cd Length: 81  Bit Score: 111.18  E-value: 2.41e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715     41 NHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPaiLFDKEFCEWMIQQIGPKLDGKI 120
Cdd:smart00920   1 VGTYGHIVYCSDYDPSGEYMFEFDGDELFYVDFDKKETVWRLPEFADFASFDYQGA--LADIAVCKANLDILIKRSNSTP 78

                   ...
gi 18765715    121 PVS 123
Cdd:smart00920  79 ATN 81
 
Name Accession Description Interval E-value
IgC1_MHC_II_alpha_HLA-DM cd21009
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
125-218 1.93e-65

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DM. Human HLA-DM, also known as H2-M in mice, plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409600  Cd Length: 94  Bit Score: 198.73  E-value: 1.93e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 125 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIV 204
Cdd:cd21009   1 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQLHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIV 80
                        90
                ....*....|....
gi 18765715 205 THEIDRYTAIAYWV 218
Cdd:cd21009  81 THEIDRYTAIAYWV 94
MHC_II_alpha smart00920
Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on ...
41-123 2.41e-31

Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 214913  Cd Length: 81  Bit Score: 111.18  E-value: 2.41e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715     41 NHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPaiLFDKEFCEWMIQQIGPKLDGKI 120
Cdd:smart00920   1 VGTYGHIVYCSDYDPSGEYMFEFDGDELFYVDFDKKETVWRLPEFADFASFDYQGA--LADIAVCKANLDILIKRSNSTP 78

                   ...
gi 18765715    121 PVS 123
Cdd:smart00920  79 ATN 81
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
41-118 4.11e-23

Class II histocompatibility antigen, alpha domain;


Pssm-ID: 460019  Cd Length: 81  Bit Score: 89.56  E-value: 4.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715    41 NHTFLH-TVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQ--EQGDAPAILFDKEFCEWMIQQIGPKLD 117
Cdd:pfam00993   1 DHVGIYgCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASfdPQGALANIAVCKNNLDILIKRSNSTPA 80

                  .
gi 18765715   118 G 118
Cdd:pfam00993  81 T 81
IGc1 smart00407
Immunoglobulin C-Type;
142-207 2.76e-18

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 76.58  E-value: 2.76e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715    142 PNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNF---TPEPSDIFSCIVTHE 207
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVtEGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHE 70
C1-set pfam07654
Immunoglobulin C1-set domain;
131-207 1.42e-16

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 72.67  E-value: 1.42e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715   131 VFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTP---EPSDIFSCIVTH 206
Cdd:pfam07654   3 VFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPsdwESGDEYTCRVEH 82

                  .
gi 18765715   207 E 207
Cdd:pfam07654  83 E 83
 
Name Accession Description Interval E-value
IgC1_MHC_II_alpha_HLA-DM cd21009
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
125-218 1.93e-65

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DM. Human HLA-DM, also known as H2-M in mice, plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409600  Cd Length: 94  Bit Score: 198.73  E-value: 1.93e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 125 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIV 204
Cdd:cd21009   1 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQLHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIV 80
                        90
                ....*....|....
gi 18765715 205 THEIDRYTAIAYWV 218
Cdd:cd21009  81 THEIDRYTAIAYWV 94
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
125-218 4.00e-41

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of the major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409424  Cd Length: 95  Bit Score: 136.67  E-value: 4.00e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 125 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCI 203
Cdd:cd05767   1 VPPEVTVFPKSPVELGEPNTLICFVDNFFPPVINVTWLRNGQPVtDGVSETVFLPREDHSFRKFSYLPFTPSEGDIYDCR 80
                        90
                ....*....|....*
gi 18765715 204 VTHEIDRYTAIAYWV 218
Cdd:cd05767  81 VEHWGLEEPLLKHWE 95
MHC_II_alpha smart00920
Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on ...
41-123 2.41e-31

Class II histocompatibility antigen, alpha domain; Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection).


Pssm-ID: 214913  Cd Length: 81  Bit Score: 111.18  E-value: 2.41e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715     41 NHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPaiLFDKEFCEWMIQQIGPKLDGKI 120
Cdd:smart00920   1 VGTYGHIVYCSDYDPSGEYMFEFDGDELFYVDFDKKETVWRLPEFADFASFDYQGA--LADIAVCKANLDILIKRSNSTP 78

                   ...
gi 18765715    121 PVS 123
Cdd:smart00920  79 ATN 81
MHC_II_alpha pfam00993
Class II histocompatibility antigen, alpha domain;
41-118 4.11e-23

Class II histocompatibility antigen, alpha domain;


Pssm-ID: 460019  Cd Length: 81  Bit Score: 89.56  E-value: 4.11e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715    41 NHTFLH-TVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQ--EQGDAPAILFDKEFCEWMIQQIGPKLD 117
Cdd:pfam00993   1 DHVGIYgCSFYQSYDPSGEYMFEFDGDELFYVDFKKKETVWRLPEFADFASfdPQGALANIAVCKNNLDILIKRSNSTPA 80

                  .
gi 18765715   118 G 118
Cdd:pfam00993  81 T 81
IGc1 smart00407
Immunoglobulin C-Type;
142-207 2.76e-18

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 76.58  E-value: 2.76e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715    142 PNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNF---TPEPSDIFSCIVTHE 207
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVtEGVSTTDPLKNSDGTYFLSSYLTVpasTWESGDVYTCQVTHE 70
C1-set pfam07654
Immunoglobulin C1-set domain;
131-207 1.42e-16

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 72.67  E-value: 1.42e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715   131 VFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTP---EPSDIFSCIVTH 206
Cdd:pfam07654   3 VFPPSPEELGKPNTLTCLVTGFYPPDITVTWLKNGQEVtEGVKTTPPSPNSDWTYQLSSYLTVTPsdwESGDEYTCRVEH 82

                  .
gi 18765715   207 E 207
Cdd:pfam07654  83 E 83
IgC1_MHC_II_alpha_HLA-DQ cd21008
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
127-206 2.48e-15

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and related proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DQ. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. Two autoimmune diseases in which HLA-DQ is involved are celiac disease and diabetes mellitus type 1. DQ is one of several antigens involved in rejection of organ transplants. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409599  Cd Length: 95  Bit Score: 69.59  E-value: 2.48e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQH--HSVpVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIV 204
Cdd:cd21008   3 PEVTVFPKSPVTLGQPNTLICLVDNIFPPVINITWLSngHSV-TEGVSETSFLSKSDHSFLKISYLTFLPSADDIYDCKV 81

                ..
gi 18765715 205 TH 206
Cdd:cd21008  82 EH 83
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
127-217 7.20e-15

Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain in beta-2-microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta-sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded, and finally excreted.


Pssm-ID: 409427  Cd Length: 94  Bit Score: 68.27  E-value: 7.20e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTH 206
Cdd:cd05770   3 PKVQVYSRFPAENGKPNVLNCYVSGFHPPDIEIRLLKNGVKIEDVEQSDLSFSKDWTFYLLKYTEFTPTKGDEYACRVRH 82
                        90
                ....*....|.
gi 18765715 207 EIDRYTAIAYW 217
Cdd:cd05770  83 NTLSEPKIYKW 93
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
136-207 3.17e-14

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 66.71  E-value: 3.17e-14
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18765715 136 PLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFG-PTFVSAVDGLSFQAFSYLNFTPEPSD---IFSCIVTHE 207
Cdd:cd00098  10 EEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVsTSSPVEPNDGTYSVTSSLTVPPSDWDegaTYTCVVTHE 85
IgC1_MHC_II_alpha_I-A cd21006
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
127-206 4.99e-14

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E a gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409597  Cd Length: 95  Bit Score: 66.25  E-value: 4.99e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVT 205
Cdd:cd21006   3 PQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVtDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVE 82

                .
gi 18765715 206 H 206
Cdd:cd21006  83 H 83
IgC1_MHC_II_alpha_HLA_DO cd21004
HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) ...
127-217 6.38e-14

HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the nonclassical MHC class II (MHCII) protein, HLA-DO, which binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the a subunit's 310 helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor by acting as a substrate mimic. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian body namely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cells indicate that it may be of physiological importance and has inspired further research. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409595  Cd Length: 95  Bit Score: 65.60  E-value: 6.38e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPT-FVSAVDGLsFQAFSYLNFTPEPSDIFSCIV 204
Cdd:cd21004   3 PRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVtEGVAQTsFYSQPDHL-FRKFHYLPFVPSAEDVYDCKV 81
                        90
                ....*....|...
gi 18765715 205 THEIDRYTAIAYW 217
Cdd:cd21004  82 EHWGLDRPLLRHW 94
IgC1_MHC_II_alpha_I-EK cd21005
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
127-206 1.93e-11

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-E. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409596  Cd Length: 95  Bit Score: 58.92  E-value: 1.93e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVT 205
Cdd:cd21005   3 PEVTVLSRSPVNLGEPNILICFIDKFSPPVVNVTWLRNGRPVtEGVSETVFLPRDDHLFRKFHYLTFLPSTDDFYDCEVD 82

                .
gi 18765715 206 H 206
Cdd:cd21005  83 H 83
IgC1_MHC_II_alpha_HLA-DR cd21007
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of ...
127-206 1.53e-10

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DR. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DR is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DRA1 and HLA-DRB1, that are adjacent to each other on chromosome band 6p21.31. Susceptibility to multiple sclerosis and rheumatoid arthritis are associated with the human histocompatibility leukocyte antigen HLA-DR2 and HLA-DR4, respectively. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409598  Cd Length: 95  Bit Score: 56.60  E-value: 1.53e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVT 205
Cdd:cd21007   3 PEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVtTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVE 82

                .
gi 18765715 206 H 206
Cdd:cd21007  83 H 83
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
127-206 6.60e-09

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain has two globular domains (N- and C-terminal) and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409423  Cd Length: 96  Bit Score: 51.95  E-value: 6.60e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPV-EGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVT 205
Cdd:cd05766   4 PSVKVSPTKTGPLEHPNLLVCSVTGFYPAEIEVKWFRNGQEEtAGVVSTELIPNGDWTFQILVMLETTPRRGDVYTCQVE 83

                .
gi 18765715 206 H 206
Cdd:cd05766  84 H 84
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
127-206 3.66e-07

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM. Human HLA-DM plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Type 1 diabetes is correlated with DM activation and it is also implicated in viral infections such as herpes simplex virus, celiac disease, multiple sclerosis, other autoimmune diseases, and leukemia. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409593  Cd Length: 97  Bit Score: 47.23  E-value: 3.66e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 127 PIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAV-DG-LSFQAFSYLNFTPEPSDIFSCIV 204
Cdd:cd21002   4 PSVRVAPTTPFNTREPVMLACHVWGFYPADVTITWLKNGDPVAPHSSAPKTAQpNGdWTYQTQVTLAVTPSPGDTYTCSV 83

                ..
gi 18765715 205 TH 206
Cdd:cd21002  84 QH 85
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
144-207 4.23e-06

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 44.63  E-value: 4.23e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18765715 144 TLVCFVSNLFPPMLTVNW--QHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPE---PSDIFSCIVTHE 207
Cdd:cd05768  20 TLTCLVKGFYPEDIFVSWlqNGEPLPSADYKTTAPVPESDGSFFVYSKLNVSTAdwnSGDVFSCVVGHE 88
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
144-207 2.62e-04

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409496  Cd Length: 99  Bit Score: 39.36  E-value: 2.62e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18765715 144 TLVCFVSNLFPPMLTVNWQHHSVPVEGfGPTFVSAV--DGLSFQAFSYLNFTPEPSD---IFSCIVTHE 207
Cdd:cd07699  20 TLVCLINKFYPGFATVTWKVDGSTVSS-GVTTSKTEqqSDNTYSMSSYLTLSSSDWNkhkVYTCEVTHE 87
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
140-207 5.57e-04

Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal.


Pssm-ID: 409428  Cd Length: 100  Bit Score: 38.24  E-value: 5.57e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18765715 140 GKPNTLVCFVSNLFPPMLTVNWQHHS-----VPVEGFGPTFVS---AVDG-LSFQAFSYLNFTPEPS-DIFSCIVTHE 207
Cdd:cd05771  14 DLPQTLSCHIAGYYPLDVDVEWLREEpggseSQVSRDGVSLSShrqSVDGtYSISSYLTLEPGTENRgATYTCRVTHV 91
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
144-207 7.13e-03

Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409495  Cd Length: 92  Bit Score: 34.90  E-value: 7.13e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18765715 144 TLVCFVSNLFPPMLTVNWQ------HHSVPVEGFGPtfvsAVDGlSFQAFSYLNFTPEPSDIFSCIVTHE 207
Cdd:cd07698  18 TLRCWALGFYPAEITLTWQrdgedqTQDMELVETRP----NGDG-TFQKWAAVVVPSGEEQRYTCHVQHE 82
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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