Results for the evaluation of the complex based on PDB Code: 3t72
Background
PDB Code 3t72 belongs to Cryo-EM structure of yeast RNA polymerase III elongation complex at 3. 9A.
The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions. Therefore, the regulation of Pol III transcription is primarily tied to the regulation of cell growth and the cell cycle, thus requiring fewer regulatory proteins than RNA polymerase II.
Therefore, the formation of the RNA polymerase III complex is required for the viability of the cell.
Computational models are represented in brown color, while the crystallographic structure is shown in cyan.
Reconstruction of the Model by Structural Superimposition.
With Structural Superimposition, the result that we obtain is very close to our original crystal structure, even taking into account that the complex we want to model is a huge complex.
Comparison between the crystal structure of 5fj8 (cyan) and the model obtained by superimposition based approach. (brown)
Animation showing the structural alignment between the crystal structure (cyan) and the superimposition-based approach model (brown)
The Structural Alignment was performed in Chimera USCF and the RMSD between 992 pruned atom pairs is 0.000 angstroms; (across all 992 pairs: 0.000)
Reconstruction of the Complex by Modeling-based approach.
Comparison between the crystal structure of 5fj8 (cyan) and the model obtained by Modeling-based approach. (brown)
Animation showing the structural alignment between the crystal structure (cyan) and the Modeling-based approach model (brown)
In this particular case, we can see that the Modeling-based approach algorithm performs more or less correctly, although not as good as the Superimposition-based approach. The Structural Alignment was performed in Chimera USCF and the RMSD between 491 pruned atom pairs is 0.628 angstroms; (across all 1422 pairs: 247.868)
