1S9V,1HDM


Conserved Protein Domain Family
IgC_MHC_II_beta

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cd05766: IgC_MHC_II_beta 
Click on image for an interactive view with Cn3D
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain
IgC_MHC_II_beta: 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. 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: 143243
View PSSM: cd05766
Aligned: 9 rows
Threshold Bit Score: 151.015
Threshold Setting Gi: 82619288
Created: 27-Jun-2007
Updated: 18-Aug-2016
Structure
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Program:
Drawing:
Aligned Rows:
 
heterodimerMHC binding
Conserved site includes 12 residues -Click on image for an interactive view with Cn3D
Feature 1:heterodimer interface [polypeptide binding site]
Evidence:
  • Structure:1HDM; human class II histocompatibility antigen (HLA-DM), Ig domain alpha/beta chain interface based on 3.5 A distance.
    View structure with Cn3D
  • Citation:PMID 9768757
  • Structure:1S9V; human class II histocompatibility antigen (HLA-DQ2), Ig domain alpha/beta chain interface, based on 3.5A distance.
    View structure with Cn3D
  • Comment:Dimerization of IgC domains from different chains is common, but not found in all members.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1             #                 ## #                          ########                   
1S9V_B        97 PTVTISPsrtealnhhNLLVCSVTDFYPAQIKVRWFRNdqeetag-vvstpliRNGDWTFQILVMLEMTPq-rGDVYTCH 174
1HDM_B        91 PSVQVAKttpfntrepVMLACYVWGFYPAEVTITWRKNgklvmhs-sahktaqPNGDWTYQTLSHLALTPs-yGDTYTCV 168
gi 122260     91 PKVRIFAlqsgslpqtDRLACYVTGFYPPEIEVKWFQNgqeeter-vvstdviQNGDWTYQVLVVLEISPr-hGDSYVCQ 168
gi 54038621  117 PNVKIVNtktldleheNLITCFVDGFFPPMIKVTWLKNgieegeq-vtssellPNGDWTFEIHVMLETTIk-hGDTFTCR 194
gi 11991786  117 PKVKVSRsnnedpnkpHMLICNVNGFYPYAITVHWYKNgqkdpgv--lssellQNGDWTGQVMVMLETSIn-pGDTFVCE 193
gi 7512211    98 PQVRIVPaqtgnpsvpIRLTCHVWGFYPPEVTIIWLHNgdivgpgdhspmfaiPNGNWTYQTQVALSVAPe-vGDTYTCS 176
gi 148734688  61 PSVTITVskqysdsqhHSLYCNTYGFYPPEIEVKWFRNnveetss-veystvyQNPDWTYQFMVMLETPLn-rGDIFTCE 138
gi 82619288  120 PSMKVFLpdivhegsiPHLVCHVWGFYPADIVVLWLLNdtilvk---nytnavPVGDWTYQIVALLDMRGslpENKYTCV 196
gi 73537142  136 PRVKISPtqsdslhhpTLLVCSVTGFYPSEIEIKWFRNgqeetag-avstellQNGDWTFQILVMLETAPr-rGDVYTCQ 213
                         90
                 ....*....|....*.
Feature 1                        
1S9V_B       175 VEHPSLQSPITVEWRA 190
1HDM_B       169 VEHIGAPEPILRDWTP 184
gi 122260    169 VEHTSLQQPITQRWEP 184
gi 54038621  195 VEHSSLQQPVSVNWVP 210
gi 11991786  194 VLHVSLDEPLRRNWDS 209
gi 7512211   177 VQHASLEEPLLEDWRP 192
gi 148734688 139 VLHSSLQSPLRVDWKP 154
gi 82619288  197 VQHSSLQDPMTEDWSY 212
gi 73537142  214 VEHASLGSPVTVQWEP 229

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