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The human PDZome represents one of the largest globular domain families in the human proteome, with 266 instances. These globular domains typically interact with C-terminal peptide motifs found in thousands of human proteins. Despite previous efforts, not all PDZ domains have experimentally solved structures and most of their complexes remain to be solved. Here, a simple and cost-effective strategy is proposed for the crystallization of PDZ domains and their complexes. A human annexin A2 fusion tag was used as a crystallization chaperone and the structures of nine PDZ domains were solved, including five domains that had not yet been solved. Finally, these novel experimental structures were compared with AlphaFold predictions and it is speculated how predictions and experimental methods could cooperate in order to investigate the structural landscapes of entire domain families and interactomes.
Supporting information
PDB references: second PDZ domain of DLG1 complexed with the PDZ-binding motif of HTLV1-TAX1, 7pc3; PDZ domain of SNTB1 complexed with the PDZ-binding motif of HTLV1-TAX1, 7pc4; third PDZ domain of PDZD7 complexed with the PDZ-binding motif of EXOC4, 7pc5; PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of PTEN, 7pc7; PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ-binding motif, 7pc8; PDZ domain of SYNJ2BP complexed with the PDZ-binding motif of HTLV1-TAX1, 7pc9; PDZ domain of SNX27 fused with ANXA2, 7pcb; PDZ domain of SNTG2 complexed with the phosphorylated PDZ-binding motif of RSK1, 7qql; PDZ domain of LRRC7 fused with ANXA2, 7qqm; PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3, 7qqn
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