SIVcpz-associated Patr-B*06:03 is related in structure and evolution to HLA-B*57:01.

<p>Shown is a neighbor-joining phylogenetic tree for the exon 2 sequences of representative <i>MHC-B</i> alleles and the four novel, nonrecombinant Gombe <i>Patr-B</i> alleles (A). An African green monkey (<i>Chlorocebus sabaeus</i>) <i>MHC-B</i> is the outgroup (<i>Chsa</i>, red) in panel A. The gray shaded box denotes the unique clade containing <i>Patr-B*06:03</i> (bold blue). This clade is maintained in trees constructed from the sequence of codons 62–74 (B), but not in trees constructed from exon 2 sequences with codons 62–74 deleted (C). This shows that codons 62–74 are the basis for the clade and the relatedness of its members. Nodal bootstrap values are based on 1,000 replications, and only values with at least 50% support are shown. Nodes that were collapsed are represented by large, black triangles. Chimpanzee alleles (<i>Patr</i>) are in blue. Also included are human (<i>HLA</i>, black), orangutan (<i>Popy</i>, pink), western gorilla (<i>Gogo</i>, green), and white-handed gibbon (<i>Hyla</i>, orange) <i>MHC-B</i>. Bonobo (<i>Papa</i>) sequences were also included in the analysis, but are within the collapsed nodes. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.s015" target="_blank">S7 Fig</a> gives the full trees with all the taxa, and the sequences are included in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.s002" target="_blank">S2 Data</a>. (D) The trans-species clade containing Patr-B*06:03 (bold blue) and HLA-B*57:01 is defined by an extensive sequence motif covering residues 25–74 of the α₂ domain. The sequences of representative MHC-B allotypes that are in the clade, or not in the clade (Other), are compared. Only positions of difference are shown. Identity to the consensus is shown by a dash, with differences from the consensus being shown by the amino acid substitution. Black-filled boxes show residues of the B pocket that bind the anchor residue at position 2 (P2) of peptide antigens [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.ref053" target="_blank">53</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.ref054" target="_blank">54</a>]. Under “Anchor” and “P2” are listed the anchor residues at P2 that are predicted to bind to each MHC-B allotype (compiled from the SYFPEITHI database of MHC ligands and peptide motifs, <a href="http://www.syfpeithi.de/" target="_blank">http://www.syfpeithi.de/</a> [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.ref055" target="_blank">55</a>] and de Groot et al. (2010) [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.ref041" target="_blank">41</a>]). Patr-B P2 residues that were inferred from known ligands are in gray italics. HLA-B*08:01 is distinguished by having a P3 anchor residue [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.ref055" target="_blank">55</a>]. Residue positions that have been associated with control of HIV are indicated by white numbers on black background [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.ref046" target="_blank">46</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002144#pbio.1002144.ref056" target="_blank">56</a>].