Supplementary data for "One clip, many genomes: how genome state may shape the use of tandem HMG-box proteins in organellar nucleoids"

Abstract

This dataset contains the underlying data and analysis files associated with the review article “One clip, many genomes: how genome state may shape the use of tandem HMG-box proteins in organellar nucleoids” by Mari Takusagawa and Yoshiki Nishimura. The deposited files support the phylogenetic and structure-based analyses presented in Figs. 2 and 3 of the article. The dataset includes: HMG-box amino-acid sequences, the MAFFT alignment, maximum-likelihood phylogenetic trees, IQ-TREE reports, and approximately unbiased (AU) test outputs underlying Fig. 2; numerical structural-similarity matrices, AlphaFold Database predicted-aligned-error matrices, and protein biophysical properties underlying Fig. 3; AlphaFold3 input specifications, predicted TFAM–DNA and HLP–DNA models, and associated confidence summaries; and the Python script and tabulated results used to estimate DNA bend angles from the predicted models. The TFAM and HLP modelling jobs used the same 30-bp DNA sequence. The bend-angle analysis fits principal axes to the outer thirds of the two DNA arms while excluding the bent apex. These computational models and analyses are provided to support inspection and reproducibility. AlphaFold3 model geometry is predictive and should not be interpreted as experimental evidence for HLP-mediated DNA bending or HBD1-mediated DNA bridging. No supplementary figures or supplementary tables are included in this deposit. A detailed description of the files, software versions and directory structure is provided in README.txt. The CC BY 4.0 licence applies to the authors’ original compilation, analyses and documentation. Third-party source data and prediction outputs remain subject to the terms of their respective providers.