1HDM,1PY4,1S9V,2BC4,1MUJ,4MD4,1A6A,2SEB,1JK8,1KTD,4I0P


Conserved Protein Domain Family
IgC1_MHC_II_alpha

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cd05767: IgC1_MHC_II_alpha 
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.
Statistics
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PSSM-Id: 409424
View PSSM: cd05767
Aligned: 27 rows
Threshold Bit Score: 135.127
Threshold Setting Gi: 109157208
Created: 29-Oct-2007
Updated: 17-Aug-2020
Structure
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Program:
Drawing:
Aligned Rows:
  next features
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:
Feature 1             # ### #                                                   # #              
1HDM_A        96 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWHDHSVPVeg-fgPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCI 174 human
1PY4_A         4 RTPKIQVYSRHPAENGKSNFLNCYVSGFYPSDIEVDLLKNGERIek-veHSDLSFSKDWSFYLLYYTEFTPTEKDEYACR 82  human
2BC4_A        99 GFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVeg-fgPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCI 177 human
1MUJ_A        89 EAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVadgvyETSFFVNRDYSFHKLSYLTFIPSDDDIYDCK 168 house mouse
1JK8_A        85 EVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVtegvsETSFLSKSDHSFFKISYLTFLPSDDEIYDCK 164 human
NP_001083579 113 GILDIKVFTLHPLTIGKPNTLVCFISNIIPPDLNITWRKNGILLtegisYTGYFALSNIEYQTFSYLNITPTYTDSYTCN 192 African clawed ...
AAF66123      82 VAPQIAMYPEEPVEWGQPNTLICLADRFYPPHISMTWLRNSEPVtdgvnITEFYIKQDYSYQRFTYLSFIPNPGDMYSCH 161 nurse shark
AAH84393     102 IAPLVNVYATKPVVLGEPNILICCVKNIFPPVMNTTWIKNGEKItdgysETSFLPAQDHSFRRLHYLAFIPNEHDIYTCE 181 African clawed ...
AAY40298     111 VTPELALFPAEAVSLEEPNVLICYADKFWPPVATMEWRRNGAVVsegvyDSVYYGRPDLLFRKFSYLPFVPQRGDVYSCA 190 chicken
AAC64371     108 DPPEIVLFSSDKVELGVENSLICFVNHFYPPSINVTWTKNGHPVstgvsLSRYFPNKDQTFHQFSTLTFTPSEGDFYSCT 187 aulonocara fort...
Feature 1                       
1HDM_A       175 VTHepdrYTAIAYWV 189 human
1PY4_A        83 VNHvtlsQPKIVKWD 97  human
2BC4_A       178 VTHeidrYTAIAYWV 192 human
1MUJ_A       169 VEHwgleEPVLKHWS 183 house mouse
1JK8_A       165 VEHwgldEPLLKHWE 179 human
NP_001083579 193 AQEg--sTTAVAYWV 205 African clawed frog
AAF66123     162 VEHeglqDPATVFWE 176 nurse shark
AAH84393     182 VEHwgleRPTRRVWK 196 African clawed frog
AAY40298     191 VRHwgaeGPVQRMWE 205 chicken
AAC64371     188 VEHsaleTPKTRIWE 202 aulonocara fort maguire

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