From 8b5adc5efe0236e0e2e51c9d57732ae7dd9e9ca3 Mon Sep 17 00:00:00 2001 From: "Craig L. Zirbel" Date: Fri, 11 Oct 2024 09:39:38 -0700 Subject: [PATCH] Add timing information for examples 1, 2, 3. --- help.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/help.md b/help.md index 04c2793..3f5f07e 100644 --- a/help.md +++ b/help.md @@ -146,7 +146,7 @@ After loading the input page, it takes 2 seconds for the Submit button to change The R3DMCS output page provides query information, a table of instances, a coordinate window, an interactive heat map, and a listing of nearby chains. Each row of the table lists one instance, and shows the PDB id, model number, chain, resolution, nearby chains, nucleotide numbers, and annotated pairwise interactions. The instances are ordered by geometric similarity so that instances that are more similar to each other are placed near one another in the table. The same ordering is used in the heatmap. The heatmap is interactive; clicking the heatmap selects instances, which are then marked in the table and are shown in the coordinate window. These features of the output page are explained in detail in the context of Example 1 below. ### Example 1: *E. coli* small decoding loop -This example illustrates the dynamic nature of the decoding loop. During translation, the decoding loop in helix 44 of the small subunit ribosomal RNA makes contact with the mRNA to promote fidelity of translation. The contact is made by two adenine bases, often numbered 1492 and 1493, flipping out of the internal loop. When the mRNA is not present, the adenine bases typically stack inside the internal loop. We can see several different conformations of the internal loop with R3DMCS. We use internal loop IL_5J7L_060 from E. coli as the query. For this illustration, we use resolution threshold 3.0Å and retrieve corresponding instances across the equivalence class of *E. coli* small subunit ribosomal RNA 3D structures. See the [URL to produce the input page for Example 1](http://rna.bgsu.edu/correspondence/comparison?selection=IL_5J7L_060&resolution=3.0&scope=EC&input_form=True). +This example illustrates the dynamic nature of the decoding loop. During translation, the decoding loop in helix 44 of the small subunit ribosomal RNA makes contact with the mRNA to promote fidelity of translation. The contact is made by two adenine bases, often numbered 1492 and 1493, flipping out of the internal loop. When the mRNA is not present, the adenine bases typically stack inside the internal loop. We can see several different conformations of the internal loop with R3DMCS. We use internal loop IL_5J7L_060 from E. coli as the query. For this illustration, we use resolution threshold 3.0Å and retrieve corresponding instances across the equivalence class of *E. coli* small subunit ribosomal RNA 3D structures. See the [URL to produce the input page for Example 1](http://rna.bgsu.edu/correspondence/comparison?selection=IL_5J7L_060&resolution=3.0&scope=EC&input_form=True). The query takes around 57 seconds to return results on 149 corresponding instances. #### Query information panel The upper left panel of the output page, shown below, shows basic information about the query and the corresponding instances. The query nucleotides come from PDB id 5J7L, model 1, chain AA. The standardized name of that chain is the small subunit ribosomal RNA, SSU for short. The query nucleotides are listed; note that residue 1407 is a modified C. Concatenating the PDB|Model|Chain with the query nucleotide sequence and number would give the full unit id, for example, 5J7L|1|AA|G|1405 for the first nucleotide. The Query Organism identifies the species of the PDB chain the query nucleotides are from. Since we chose to retrieve instances from across the equivalence class, the equivalence class identifier NR_3.0_56726.109 is shown; this indicates that the resolution threshold is 3.0Å and that the equivalence class with handle 56726 is on version 119, meaning that since the inception of this equivalence class, the membership has changed 119 times. This query has retrieved 134 instances, all of which are from *E. coli* small subunit ribosomal RNA 3D structures. In the all-against-all geometric comparison, the largest geometric discrepancy is 1.40, indicating a moderate level of geometric similarity even between the most dissimilar instances. @@ -220,14 +220,14 @@ This [example](http://rna.bgsu.edu/correspondence/comparison?selection=IL_5AJ3_0 Note that 6GAZ is the representative structure. Note here that the chains in this equivalence class map to Rfam family RF00177, which Rfam labels as being bacterial SSU, but which mitochondrial and chloroplast ribosomes also match well, due to the ribosomes in those organelles originating from bacteria. -Using 5AJ3 as a starting point in the query, R3DMCS maps its 18 nucleotides to other 3D structures which also map to [Rfam family RF00177](https://rfam.org/family/SSU_rRNA_bacteria). The query has depth=1, so only on structure, the representative structure, from each equivalence class is returned. Thus an instance from 6GAZ appears in the output page, not the query from 5AJ3. +Using 5AJ3 as a starting point in the query, R3DMCS maps its 18 nucleotides to other 3D structures which also map to [Rfam family RF00177](https://rfam.org/family/SSU_rRNA_bacteria). The query has depth=1, so only on structure, the representative structure, from each equivalence class is returned. Thus an instance from 6GAZ appears in the output page, not the query from 5AJ3. The query takes about 17 seconds to return results on 27 corresponding instances. This loop is particularly interesting, because the heat map shows four structures that are quite distinct from the rest, see below where we have selected the instance from 6GAZ and the instance from 5J7L, which is from *E. coli* as in previous examples. The key difference is that the four structures in the lower right of the heat map are all mitochondrial ribosomes, in which position 4 in the sequence is C, whereas the other structures all have G in that position. This example shows that when the G in the base triple in the G-bulge changes to C, the base triple is lost, and the C bulges out of the motif. Apparently that is not a problem in some mitochondria, but all bacteria in the 3D structure database have G in that position, and the G participates in the base triple. ![Example2](/assets/example2.png) ### Example 3: *E. coli* LSU H34 hairpin loop -[Example 3](http://rna.bgsu.edu/correspondence/comparison?selection=HL_8GLP_022&exp_method=all&resolution=4.0&depth=3&scope=Rfam&input_form=True) illustrates the GNRA hairpin loop from Helix 34 of the large subunit ribosomal RNA, compared across different species in the associated Rfam family solved at resolution 4.0A or better, with up to 3 instances from each species. This example illustrates how some structures (in this case, the models of *Triticum aestivum*) model the top adenine base of the GNRA in syn while others model that base in anti. Other variability is also evident. The image below shows the query instance from 8GLP (human) and one instance with the top A modeled in syn; the syn/anti superposition makes a characteristically symmetric image which can be spotted relatively easily. Modeling differences such as this often explain the difference between clusters of instances. +[Example 3](http://rna.bgsu.edu/correspondence/comparison?selection=HL_8GLP_022&exp_method=all&resolution=4.0&depth=3&scope=Rfam&input_form=True) illustrates the GNRA hairpin loop from Helix 34 of the large subunit ribosomal RNA, compared across different species in the associated Rfam family solved at resolution 4.0A or better, with up to 3 instances from each species. This example illustrates how some structures (in this case, the models of *Triticum aestivum*) model the top adenine base of the GNRA in syn while others model that base in anti. Other variability is also evident. The image below shows the query instance from 8GLP (human) and one instance with the top A modeled in syn; the syn/anti superposition makes a characteristically symmetric image which can be spotted relatively easily. Modeling differences such as this often explain the difference between clusters of instances. This query takes about 7 seconds to return results on 14 corresponding instances. ![Example3](/assets/example3.png)