DOI: 10.5281/zenodo.15212923
title: Data associated with the submitted manuscript "Uncovering hidden functional states in Cryo-EM datasets with EMPROVE"

description: Here we include datasets associated with the application of EMPROVE, a cryo-EM data processing pipeline for particle selection and 3D class reassignment in structural biology. The deposited data include: EMPIAR-10308, featuring the serotonin 5-HT1BR-Go receptor complex, used to assess EMPROVE-based particle selection; a focused analysis on the ligand-binding pocket from the same dataset; EMPIAR-10667, applied to the 46Q HTT-HAP40 complex to evaluate orientation bias correction and conformational resolution; and a newly acquired Group II intron dataset processed with EMPROVE for RNA structure analysis. Raw particle stacks from EMPIAR-10308 and EMPIAR-10667 are alredy publicly deposited (thus not included in this archive), and EMPROVE-based particle selection for these datasets is included. For the Group II intron dataset, particle stacks for J317 and J246 are provided. Datasets also include EMPROVE-refined 3D maps and related metadata.

EMPIAR_10308_EMPROVE_particle_selection.zipThis archive contains EMPROVE-based particle selection results applied to EMPIAR-10308 (serotonin 5-HT1BR-Go receptor complex bound to donitriptan). It also includes halfmaps, modelAngelo automatic models obtained from the unprocessed maps, and the "*_stackNotationEMPIAR.star" star files for particle stacks corresponding to the subset of particles ranked and selected using EMPROVE. Directories include deposited_data: corresponding to the original EMPIAR-10308 deposit. selected_244565_particles, with EMPROVE-selected subset, and the selected_244565_particles_refined: with the included angular refined maps reconstructed from the selected particles.

EMPIAR_10308_ligand_classReassignment.zipThis archive includes focused classification and reassignment data for the ligand-binding region of the 5-HT1BR-Go receptor complex from EMPIAR-10308. Files include particle stacks, class assignments, and refined maps corresponding to the five final classes identified in Figure S3 of the manuscript, in support to a comparative evaluation of conformational states within the binding pocket. The archive contains refined maps (half maps and post-processed maps), local resolution estimations, corresponding .star files of particles contributing to each class, and the new the pdb model associated with the ligand.

EMPIAR_10667_final_classes_selected.zip and EMPIAR_10667_3dFSC_analysis.zipThese archives contain EMPROVE-based class reassignment and 3D refinement results for EMPIAR-10667 (46Q HTT-HAP40 complex). Particular focus is given to flexible regions such as the N-terminal BΦ motif, and domain-resolved refinements are available for further comparative analysis. Included files are final refined maps for each selected class, modelAngelo for each selected class, .star files of selected particles, local resolution maps, directional 3D FSC volumes and correlation plots. Atomic models corresponding to each class, including mask and map fitting metadata.

groupII_intron.zipThis dataset includes newly acquired cryo-EM data for the Oceanobacillus iheyensis Group II intron, processed with EMPROVE, with the aim to facilitate detailed exploration of conformational heterogeneity in the catalytic core and peripheral regions. The archive contains particle stacks for J317 and J246. Furhter, it contains the seven EMPROVE-refined 3D classes, and associated data: metadata star files of particles assigned to each class, full and half maps for all classes,  masks, local resolution maps and FSC plots, validation reports for deposited maps on pdb, data processing summary, comparative resolution data against standard classification.