Representative simulated trajectories from: Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome
Data files
Mar 24, 2026 version files 60.42 GB
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8cgn_7.6mM_Mg.pdb
19.90 MB
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README.md
2.39 KB
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rotated_rep_traj.dcd
29.82 GB
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unrotated_rep_traj.dcd
30.58 GB
Abstract
This data set includes representative trajectories and a reference PDB that were generated for use with the SMOG+inner-ion model (Wanes et al. 2026). In the force field, the rotated and unrotated conformations of the eukaryotic ribosome were defined to be stable, and explicit electrostatics and ions were also included. To model ion-RNA interactions, effective potentials were defined that ensure the local distribution of divalent ions is consistent with experimental measures for smaller model RNA systems. In this specific data set, the trajectory files represent the final simulated segments of umbrella simulations for the rotated and unrotated ensembles. The umbrella was introduced to sample distinct states of rotation, though the ions were free to associate/dissociate.
Dataset DOI: 10.5061/dryad.g4f4qrg4r
Description of the data and file structure
This repository contains representative trajectories of the unrotated and unrotated states of the eukaryotic ribosome, simulated using the SMOG+inner-ion model. The repo also has a reference PDB file that can be used to visualize the trajectories.
The PDB and DCD files have been visualized using VMD and analyzed using MDtraj.
This dataset contains three files:
8cgn_7.6mM_Mg.pdb : A PDB file of the complete eukaryotic ribosome structure, with ions, as used for production simulations at [MgCl2] = 7.6 mM.
unrotated_rep_traj.dcd : Representative simulation of the unrotated ensemble. This is the final simulated segment of the published trajectory with an umbrella potential centered at -0.5.
rotated_rep_traj.dcd : Representative simulation of the rotated ensemble. This is the final simulated segment of the published trajectory with an umbrella potential centered at 0.4.
Files and variables
File: rotated_rep_traj.dcd
Description: Representative simulation of the rotated ensemble. This is the final simulated segment of the published trajectory with an umbrella potential centered at 0.4.
File: unrotated_rep_traj.dcd
Description: Representative simulation of the unrotated ensemble. This is the final simulated segment of the published trajectory with an umbrella potential centered at -0.5.
File: 8cgn_7.6mM_Mg.pdb
Description: A reference structure that can be used to visualize the trajectory files. This is a PDB file of the complete eukaryotic ribosome structure, with ions, as used for production simulations at [MgCl2] = 7.6 mM. It is derived from PDB entry 8CGN. However, there were several modifications required to make it compatible with the simulations. First, the tRNA molecule was removed. Second, some modified residues were converted to their unmodified forms. Third, only atoms that were common between PDB ID 8CGN and 8CCS were included. Atoms unique to 8CGN were removed. Finally, Mg2+, Cl - and K+ atoms were added, such that [KCL] = 100 mM and [MgCl2] = 7.6 mM.
Code/software
Visual Molecular Dynamics - version 1.9 and higher.