Model Evaluation: 6gmh

Results for the evaluation of the complex based on PDB Code: 6gmh

Background

Code 6gmh in PDB, corresponds to Structure of activated transcription complex Pol II-DSIF-PAF-SPT6

Gene regulation involves activation of RNA polymerase II (Pol II) that is paused and bound by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we show that formation of an activated Pol II elongation complex in vitro requires the kinase function of the positive transcription elongation factor b (P-TEFb) and the elongation factors PAF1 complex (PAF) and SPT6.

The cryo-EM structure of an activated elongation complex of Sus scrofa Pol II and Homo sapiens DSIF, PAF and SPT6 was determined at 3.1 Å resolution and compared to the structure of the paused elongation complex formed by Pol II, DSIF and NELF. PAF displaces NELF from the Pol II funnel for pause release. P-TEFb phosphorylates the Pol II linker to the C-terminal domain. SPT6 binds to the phosphorylated C-terminal-domain linker and opens the RNA clamp formed by DSIF. These results provide the molecular basis for Pol II pause release and elongation activation. (Vos SM et al.)

Project files

4MB

6gmh.pdb

Crystal Structure for 6gmh

3MB

complex.pdb

Superimposition-based approach 6gmh

6MB

6gmh_modeller.pdb

Modeling-based approach model 6gmh

Reconstruction of the Model by Structural Superimposition.

Comparison between the crystal structure of 6gmh (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)

Reconstruction of the Complex by Modeling-based approach.

Comparison between the crystal structure of 6gmh (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)

The Modeling-based algorithm, give us a model with some missing chains. Although the globular core of the protein is more or less made, a lot of chains are not included in the complex, giving us an incorrect result.