Extract, store and use your own 3D motifs

During the construction of an RNA 3D model, the most difficult (and important) step is probably the ability to find 3D folds that fit for single-strand regions. Single-strands link and orient your helices, having consequently a great impact on your RNA 3D model. With Assemble2, i introduced an interactive way to find such 3D folds. By clicking on a single-strand region, Assemble2 pops up a list a 3D folds with identical length and topology (apical loop, inner loop, 3-way junction,…). In the screenshot below, i have loaded the sample file named ft3100_from_FANTOM3_project.fasta and i have double-clicked on a residue of an apical loop of length 7.

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Several users wanted to be able to store and use their own RNA motifs, like you could in Assemble1. Starting with the last daily build (Sep 23, 2013), this ability is now back. As an example, i will extract, store and apply an apical loop extracted from the yeast 25S rRNA (PDB ID: 3O5H).

Once the 3D structure opened, i’m selecting the residues making my 3D motif. I’m including the last base-pair of the helix to have it in common with the helix i will create de novo in my 3D model.

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I’m opening the lateral panel named “CreateRNAMotif”. Once a screen capture of the motif done, a name and a category defined, i’m clicking on the button “Create motif” to make it appear in the lateral panel named “MyMotifs”.

capture3

Now, i’m opening my RNA to model (and stored in the file named ft3100_from_FANTOM3_project.fasta). I’m selecting an helix and i’m creating it in 3D.

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In the panel “MyMotifs”, i’m right-clicking on my new motif and i’m choosing “Get details”. The lateral panel named “MotifDetails” is opening. This motif is made with only one sequence of 9 contiguous residues. I’m selecting my apical loop, along with the two residues making the last base-pair in the helix (left-click on G47 and shift+left-click on C55). The residues making this base-pair are already present in Chimera (look at the green halo in the 3D scene).

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I’m clicking on the button “Link” in the panel “MotifDetails” and then on the button “Apply”.

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It’s done. Several remarks:

  • when you create a motif, Assemble2 stores all the tertiary interactions stabilizing it. These interactions are added automatically to your 3D model when the motif is applied,
  • when you apply a motif, Assemble2 searches for residues already present in the 3D scene to fit the new residues to the current 3D model. If no such residues are available, the new residues will be created with their original 3D coordinates (and will be located “somewhere” in the 3D scene),
  • by right-clicking on a motif in the panel “MyMotifs”, you will see a choice named “Load 3D”. This will load the 3D structure into Chimera and highlight the residues making the motif. For now, Assemble2 loads it into the layer #10 of Chimera. Consequently, Assemble2 can be used to keep track of interesting 3D motifs. This is something you didn’t have with Assemble1,
  • if your motif contains non-contiguous residues, Assemble2 will store it with several “Motif sequences” (meaning several set of contiguous residues). You will have to link each motif sequence to be able to apply its 3D fold.
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