Note: This page contains background about the sourcing of our atomic coordinates. Feel free to skip ahead to Substitutions and Modifications to begin your experiments.
The structures that are the departure point for our Molecular Dynamics (MD) studies are cryo-EM images of five ribosome translocation stages, published by the Korostelev group. Briefly, cryo-EM is a method where an aqueous solution of the macromolecule is frozen, then an electron beam is passed through the sample and picked up by a detector. A computer then takes all of the images of the proteins in solution (in various orientations) and stitches them together to make a 3D structure. The PDBs below can therefore be considered average structures at energy minima along the translocation reaction coordinate. They are resolved at 3.5 - 4.2 angstroms, while for reference a carbon-carbon single bond length is about 1.5 angstroms. Cryo-EM is only sensitive enough to resolve heavy atoms (not hydrogen), and residues that are part of flexible chains can also be problematic. They are sometimes not resolved or they are grown in based on the known amino acid/nucleotide sequence. For these reasons, these static structures have serious limitations in understanding dynamic phenomena, which we overcome using MD.
Stage I / 5JUO
Stage II / 5JUP
Stage III / 5JUS
Stage IV / 5JUT
Stage V / 5JUU
It is important to note that these structures contain an IRES, a viral tRNA and mRNA mimic. We have visually analyzed the similarity of the IRES conformation to a real tRNA/mRNA in the ribosome, and they are very similar in the vicinity of the A site (which is also supported by the fact that the IRES can act as an analog at all), but begin to deviate 5-10 residues away from the tRNA "anticodon." Therefore, caution should be used when interpreting data about "tRNA" structure in our system at a significant distance from the A site.
Understanding PDB Files
If you open a PDB file, you will see the coordinates and identifiers for each atom in the system. A sample line:
ATOM 265 HO5' U 3 172.950 259.409 225.896 1.00 0.00 H
ATOM - flag that line contains coordinates
265 - atom index/number
HO5' - atom identifier, specific to each residue, in this case the hydrogen attached to the oxygen of a sugar
U - residue type, in this case uracil
3 - residue number
172.950 259.409 225.896 - x,y,z coordinates
1.00 - occupancy, fraction of atoms with this conformation, used if an atom has multiple major possible positions
0.00 - b-factor, variability of position, usually not provided but can be re-coded to display certain properties using PyMol
H - element type
Continue on to Subsystem Initialization to learn more about the development of Neighborhood 2, or skip ahead to Substitutions and Modifications to begin your experiments.
