AlphaFold3-predicted structures of the AAG/UV-DDB complex in the absence and presence of abasic site-containing DNA

This dataset contains AlphaFold3-predicted structural models of the UV-DDB/AAG protein complex generated in support of the manuscript "UV-DDB as a Dynamic Regulator Linking Base Excision and Nucleotide Excision Repair via AAG Interaction." All predictions were performed using the AlphaFold3 web server (https://alphafoldserver.com) with full-length protein sequences submitted as separate entities: human DDB1 (UniProt Q16531), human DDB2 (UniProt Q92466), and human AAG (UniProt P29372). The dataset includes five predicted structural models: 1. DNA-free wild-type model (UV-DDB/AAG complex in the absence of DNA): The highest-ranked model selected based on pTM and ipTM scores, used for identification of putative contact residues at the DDB1/AAG interface. 2. DNA-free DDB1(Glu800Ala) mutant model: Alanine substitution at DDB1 Glu800, predicted to abolish simultaneous engagement of AAG Arg145 and Lys229. 3. DNA-free AAG(Arg145Ala) mutant model: Alanine substitution at AAG Arg145, predicted to disrupt contacts with DDB1 Glu800 and Thr798. 4. DNA-free AAG(Lys229Ala) mutant model: Alanine substitution at AAG Lys229, predicted to disrupt contacts with DDB1 Gln759 and Glu800. 5. DNA-bound ternary complex model (AAG/UV-DDB/DNA complex): Predicted structure incorporating a double-stranded AP site-containing DNA substrate (THF37, 37-mer), with the complementary strand generated using the reverse complement function of the AlphaFold3 server. This model was used for analysis of AAG active site residue positioning relative to the AP site. All models are provided as .cif files corresponding to the top-ranked prediction from each AlphaFold3 run. Confidence metrics (pTM, ipTM, and PAE plots) for each model are provided in the Supplementary Information of the associated manuscript.