Alphafold structural models for putative Phytoplasma Effectors (PhAMEs)

Description

This dataset contains AlphaFold2 v2.2 models, AlphaFold-Multimer v3 models, and sequences of putative Phytoplasma Effectors (PhAMEs). These models support the research published in “Effector Innovation in Genome-Reduced Phytoplasmas and Other Host-Dependent Mollicutes” by Mirkin et al. (https://doi.org/10.1101/2025.07.14.664665).

Dataset Contents

PhAMEs_pdb.zip — Contains the PDB files of the top-ranked AlphaFold-predicted structures of phytoplasma predicted secreted proteins (PhAMEs). The names of the pdb files within PhAMEs_pdb.zip correspond to those found in Column A/B of S4 table in Mirkin et al. (https://doi.org/10.1101/2025.07.14.664665).

PhAMEs_Seq_mature.fasta — Corresponds to a multifasta file with the mature PhAME sequences found in Column A/B in S4 table of Mirkin et al. (https://doi.org/10.1101/2025.07.14.664665).

SAP54_OY-M-AFM.zip — Contains the AlphaFold-Multimer v3 structural predictions for the protein–protein interactions between SAP54/PHYL1 from ‘Candidatus Phytoplasma asteris’ OY-M and AtRAD23c, the C-terminal domain of AtRAD23c, or AtSEP3. These files correspond to Figure 3 and S10 Fig of Mirkin et al. (https://doi.org/10.1101/2025.07.14.664665).

AtTCP10_SAP11_0ef1.zip — Contains the AlphaFold-Multimer v3 structural predictions for the protein–protein interactions between SAP11 from ‘Candidatus Phytoplasma asteris’ AYWB and AtTCP10. These files correspond to S15 Fig of Mirkin et al. (https://doi.org/10.1101/2025.07.14.664665).

For the AlphaFold-Multimer structural predictions, all standard ColabFold outputs are included:

Five structural models (.pdb files) ranked by confidence

Confidence score files (.json) for each model

Multiple sequence alignment (.a3m file)

Predicted aligned error data and visualizations (.json, .png)

Coverage analysis and confidence plots (.png)

Configuration and environment files