Model Evaluation: 1o4x

Results for the evaluation of the complex based on PDB Code: 1o4x

Background

PDB Code 1o4x belongs to a ternary complex of the DNA binding domains of the OCT1 and SOX2 transcription factors, with a 10mer oligonucleotide from the HOXB1 regulatory element.

Dimerization of OCT1 and SOX2 is important because they synergistically regulate developmental genes, and the combined action from both of them is required for the correct genetic expression during embryogenesis.

Also the combination of both, is related to a role of neural development and cell selfrenewal, making this interaction critic for life.

This complex is made by the combination of two different protein chains (OCT1 and SOX2), that belong to different transcription factors, and binds to two DNA strands. We have 4 chains in this complex. Model is represented in brown color, while the crystallographic structure is shown in cyan.

Project files

407KB

1o4x.pdb

Crystal structure 1o4x

343KB

1o4x_superimposition.pdb

Superimposition-approach model

343KB

1o4x_modeller.pdb

Modeller-approach model

Reconstruction of the Model by Structural Superimposition.

Comparison between the native structure of 1o4x and the model obtained by superimposition.

Animation showing the structural alignment between the Superimposition obtained model and the native structure.

This complex is a small heteromer complex, meaning that there is no confusion between identical chains placed in different parts of the protein. This was a first test as an easy complex for our algorithm, and only seeing the images we can see that it performed really well.

Structural alignment was performed with MatchMaker algorithm from Chimera USCF software, which results in an RMSD between 129 pruned atom pairs of 0.000 angstroms; (across all 129 pairs: 0.000)

Reconstruction of the Complex by using Modeller.

We also checked the complex generated by our Modeller-based algorithm, which gave us the next results:

Comparison between the native structure and the one obtained by a Modeller-based algorithm

Animation showing the structural alignment between the native structure and the modeller-based algorithm model.

In this case, our modeller-based approach performed very well, and when performed the structural alignment with Chimera USCF, the RMSD between 127 pruned atom pairs is about 1.054 angstroms; (across all 129 pairs: 1.092)