Model Evaluation: 5nss

Results for the evaluation of the complex based on PDB Code: 3t72

Background

The PDB Code 5nss corresponds to Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex.

Members of the protein family called ATPases associated with various cellular activities (AAA(+)) play a crucial role in transforming chemical energy into biological events. AAA(+) proteins are complex molecular machines and typically form ring-shaped oligomeric complexes that are crucial for ATPase activity and mechanism of action.

The Escherichia coli transcription activator phage shock protein F (PspF) is an AAA(+) mechanochemical enzyme that functions to sense and relay the energy derived from nucleoside triphosphate hydrolysis to catalyze transcription by the sigma(54)-RNA polymerase. Closed promoter complexes formed by the sigma(54)-RNA polymerase are substrates for the action of PspF. (Bordes P. et al)

Project files

3MB

5nss.pdb

Crystal Structure for 5nss

2MB

5nss_model.pdb

Superimposition-based approach Model 5nss

Reconstruction of the Model by Structural Superimposition.

Comparison between the crystal structure of 5nss (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)

In this case, the Superimposition-based approach algorithm, perform correctly some parts of the protein, like most polypeptide chains. However it did not add one of the types of chains (It did not add any of a type of homologous sequences), and also did not add correctly the DNA.

The algorithm tried to add these chains, however it found them to violate some restraints.

After checking the algorithm, we reached the conclusion that the most probable opinion is that the parsing of the original PDB was not made correctly for that chains, due to some unique features in these chains. However, we could not find the bug yet.