3BIK,3BP6,2M2D


Conserved Protein Domain Family
IgV_PD1

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cd16088: IgV_PD1 
Click on image for an interactive view with Cn3D
Immunoglobulin (Ig)-like domain of Programmed cell Death 1 (PD1)
Programmed cell Death 1 (PD1, also known as CD279 or cluster of differentiation 279) is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands.
Statistics
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PSSM-Id: 319337
View PSSM: cd16088
Aligned: 5 rows
Threshold Bit Score: 190.881
Threshold Setting Gi: 507986249
Created: 21-Apr-2015
Updated: 18-Aug-2016
Structure
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Program:
Drawing:
Aligned Rows:
 
PD-1/PD-L1PD-1/PD-L2
Conserved site includes 21 residues -Click on image for an interactive view with Cn3D
Feature 1:PD-1/PD-L1 complex [polypeptide binding site]
Evidence:
  • Structure:3BIK: mouse PD1 binds ligand PD-L1, contacts at 4A
    View structure with Cn3D
  • Comment:PD-1/PD-L1 complex resembles the antigen-binding Fv domains of antibodies and T cell receptors

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                   # # #    #### #    ## # # #          
3BIK_B        12 LTFYpaWLTVSEGANATFTCSLsnw--------------sedLMLNWNRLspSNQTEKQAAFSNGLSQPVqdarFQIIQL 77
3BP6_A         2 LTFYpaWLTVSEGANATFTCSLsnw--------------sedLMLNWNRLspSNQTEKQAAFSNGLSQPVqdarFQIIQL 67
2M2D_A         3 PTFSpaLLVVTEGDNATFTCSFsnt--------------sesFVLNWYRMspSNQTDKLAAFPEDRSQPGqdsrFRVTQL 68
gi 507986249  74 PTISpaRLSVPEGGNASFTCSLshdalptphdtqpaprdtqqARLNWYRLgpGNQSSKLAAFPEDQHQAGqdwrFRVTPL 153
gi 505854506  28 PNSSpvQLSVTEGANVSFTCHFptk--------------sgfPQFNWYRLcpGNRTEKLAAYPKEQGQHGrrwhVTATNL 93
                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
Feature 1                             # #   # ### # #        
3BIK_B        78 pnrhDFHMNILdtrrndsGIYLCGAIsLHPKAKIEESPGAELVV 121
3BP6_A        68 pnrhDFHMNILdtrrndsGIYLCGAIsLHPKLKIEESPGAELVV 111
2M2D_A        69 pngrDFHMSVVrarrndsGTYLCGAIsLAPKAQIKESLRAELRV 112
gi 507986249 154 pggrDFLLTLVgarphdsGTYLCVAIyLNPRVHFSESPHIKLTV 197
gi 505854506  94 sathNFHMHLLsaqqndsGLYRCAAIyLHPEIHILESHMQLNVT 137

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