1HDM,1A6A,1S9V,2BC4


Conserved Protein Domain Family
IgC_MHC_II_alpha

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cd05767: IgC_MHC_II_alpha 
Click on image for an interactive view with Cn3D
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain
IgC_MHC_II_alpha: Immunoglobulin (Ig) domain of 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. In both humans and in mice these molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), for example on B-lymphocytes, monocytes, and macrophages. 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 protelytic 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.
Statistics
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PSSM-Id: 143244
View PSSM: cd05767
Aligned: 12 rows
Threshold Bit Score: 143.635
Threshold Setting Gi: 147902886
Created: 29-Oct-2007
Updated: 18-Aug-2016
Structure
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Program:
Drawing:
Aligned Rows:
 
heterodimerMHC binding
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:heterodimer interface [polypeptide binding site]
Evidence:
  • Comment:Dimerization of IgC domains from different chains is common, but not found in all members.
  • Structure:1HDM; human class II histocompatibility antigen (HLA-DM), alpha/beta chain interface between IgC domains, based on 3.5 A distance.
    View structure with Cn3D
  • Citation:PMID 9768757
  • Structure:1S9V; human class II histocompatibility antigen (HLA-DQ2), alpha/beta chain interface between IgC domains, based on 3.5A distance.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1            # ### #                                                   # #               
1HDM_A        97 FPIAEVFTLKPLEFGkpNTLVCFVSnlfPPMLTVNWHDHSVPVEg-FGPTFVSAvdglSFQAFSYLNFTPepSDIFSCIV 175
1A6A_A        82 PPEVTVLTNSPVELRepNVLICFIDkftPPVVNVTWLRNGKPVTtgVSETVFLPredhLFRKFHYLPFLPstEDVYDCRV 161
1S9V_A        88 VPEVTVFSKSPVTLGqpNILICLVDnifPPVVNITWLSNGHSVTegVSETSFLSksdhSFFKISYLTLLPsaEESYDCKV 167
gi 147902886 114 ILDIKVFTLHPLTIGkpNTLVCFISniiPPDLNITWRKNGILLTegISYTGYFAlsniEYQTFSYLNITPtyTDSYTCNA 193
gi 150247073 115 IPVADVFLQQPLQLGypNTLICMVGnifPPAITISWQRDGIPVTdgVTHLTYTPtedlGFMRFSYLAVTPhsGDIYACIV 194
gi 63259186  112 TPELALFPAEAVSLEepNVLICYADkfwPPVATMEWRRNGAVVSegVYDSVYYGrpdlLFRKFSYLPFVPqrGDVYSCAV 191
gi 54038108  103 APLVNVYATKPVVLGepNILICCVKnifPPVMNTTWIKNGEKITdgYSETSFLPaqdhSFRRLHYLAFIPneHDIYTCEV 182
gi 3764099   109 PPEIVLFSSDKVELGveNSLICFVNhfyPPSINVTWTKNGHPVStgVSLSRYFPnkdqTFHQFSTLTFTPseGDFYSCTV 188
gi 26984522   92 PPWTTVYSRNDVKLNvkNTLICHVTgffPPPVRVLWTKNNVNVTdgSTISRYYPnkdgTMNVFSRLSFIPeeGDVYGCSV 171
gi 7658281    83 APQIAMYPEEPVEWGqpNTLICLADrfyPPHISMTWLRNSEPVTdgVNITEFYIkqdySYQRFTYLSFIPnpGDMYSCHV 162
gi 199584370 114 APEVKVFSENPVELGepNILICFVDkfsPPVLNITWLKNGKEMTdgVFETDFYPrqdnAFRKFTYLPFIPttDDYYDCRV 193
2BC4_A       100 FPIAEVFTLKPLEFGkpNTLVCFVSnlfPPMLTVNWQHHSVPVEg-FGPTFVSAvdglSFQAFSYLNFTPepSDIFSCIV 178
                         90
                 ....*....|....
Feature 1                      
1HDM_A       176 THepdrytAIAYWV 189
1A6A_A       162 EHwgldepLLKHWE 175
1S9V_A       168 EHwgldkpLLKHWE 181
gi 147902886 194 QEgs--ttAVAYWV 205
gi 150247073 195 TRerdnisVVAYWV 208
gi 63259186  192 RHwgaegpVQRMWE 205
gi 54038108  183 EHwglerpTRRVWK 196
gi 3764099   189 EHsaletpKTRIWE 202
gi 26984522  172 EHkalqqpQTRTWD 185
gi 7658281   163 EHeglqdpATVFWE 176
gi 199584370 194 EHwglakpFLKHWE 207
2BC4_A       179 THeidrytAIAYWV 192

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