Four structures are represented here docked on one another based on positioning the alpha-carbons of the residues that are equivalent according to the above alignment. Specifically, Rpr2 was used as a baseline to move each of the others to make the final multi-model file.

The structures represented are:

• Rpr2p from the Yeast RNase P cryo-EM structure (PDB ids: 6ah3 and 6agb)

• Theoretical model of yeast Snm1p based on the structures of Rprp2p and archaeal Rpp21p.

• Archaeal Rpp21p (PDB id: 1x0t)

• Rpa12p (Rrn4p) from the 3.27 Å crystal structure of RNA Pol I (PDB id: 4c3h)

The Jupyter notebook to generate the code used to make the superimposed structures using the alignment (shown above) can be viewed here.

There is a structural feature common to all of them. It is highlighted by loops that coordinate zinc that are adjacent a three stranded beta-sheet.

(Seems it would be classified as a 'zinc ribbon', related in some way to the sub-family zinc ribbon domains. I base this on Fernández-Tornero et al. ‎2013 pointing out " C-terminal Zn ribbon of subunit A12.2" ^[1]. Other support for that terminology is found in Krishna et al, 2003 ^[2] and Filhol et al 2013 ^[3]. However, the feature in the Rpr2p homologs and RNA pol subunits overlay better than the other examples I have come across, and so I didn't 'commit' to that term yet as perhaps it doesn't adequately reflect the relationship.)

(In the case of Snm1p, it is expected to do that. No zinc was in the model and so I left the zinc from Rpr2p showing when that model is highlighted alone.)

Using the following scene, I load all the four structures as grey to start at a basic point in order to subsequently emphasize the structural feature in each by highlighting it with the rest of the protein translucent.
Click on the green scene link below to trigger the scene and work through subsequent scene links and toggles to see more.

Colors of the structural features per chain:

• Rpr2p

• Snm1p (theoretical)

• Rpp21p

• Rpa12p (Rrn4p)

I kept the zinc ions colored by element (CPK) throughout since the spheres are obvious.

Because it can be hard to see each relative the others, click the scene below entitled 'Start with just Rpr2p shown' to start off with Rpr2p shown and then use the toggles below to selectively turn on/off individual chains and display combinations.

Controls for the feature in specific chains:

(Because Rpr2p and Snm1p are sharing the zinc here, when Snm1p gets toggled off it will hide the shared zinc. Just cycle through pressing the Rpr2p toggle until it goes back on, if you need it when Rpr2p is shown.)

The feature in the context of each chain

In order emphasize the similar structural feature, above I had the rest of each protein barely visible. This scenes in this section turn each of those back on and allow combinations of them to be toggled off or on. I color the full chain for each a similar color as the feature portion, however, I vary the shade somewhat so that the feature and the rest of each chain are distinguishable when inspected closely.

Colors per chain:

• Rpr2p

• Snm1p (theoretical)

• Rpp21p

• Rpa12p (Rrn4p)

Click the scene below entitled 'Start with just Rpr2p shown' to start off with Rpr2p shown and then use the toggles below to selectively turn on/off individual chains and display combinations.

Controls for specific chains:

Summary Image

Direct Link to the full size