RNA polymerase of sars cov2
Replication of genetic material to inherit to offspring is a complex procedure: information directed synthesis with the requirement for exactness. Also RNA viruses have to be picky, else they won't recognize their offspring. The RNA polymerase used is therefore of a special structure.
The tube found in this complex symbolizes the ribonucleic acid (RNA) in the . The protein part consists of the polymerase proper (similar in all RNA viruses) named nsp12 in cov2 and depicted here in blue. Additionally here are nsp7 (pink) and twice nsp8 (green and yellow). Here it may look like the proteins are coiled like a ball of wool, but really they harbour an inner structure , wich is kept by forces between the individual amino acids. You may discern different kinds of structure . Wound regions (red) similar to screws are called helices; if the protein chain is ordered in a parallel fashion (yellow) it is named a folded sheet. In nsp7 there are only helical regions.
More interesting is the structure of nsp12
. You have the impression a hand clasps the nucleic acid. The regions of the molecule were named accordingly:
,
and
. The secondary structure shows mainly helical parts
.
For the activity of the enzyme the shape of the active center is important
. For a better view we make the Protein somewhat more translucent
. The template RNA strand (blue) is paired to the already synthesized new strand (red). The "empty" space between the
and the end of the red RNA strand is waiting for the next fitting RNA component to prolong the RNA chain. Because of the biochemical pairing properties of the RNA components an negative copy of the original strand is produced. Only in a further replication round a positive sense copy of the negative strand can be made. What a waste of material! That is the price for the simple pattern of single strand RNA viruses. (With the mouse you may turn the view to other aspects.)
this demonstration.
Literature:
H S Hillen et al, Nature 584, 154-156 (2020), DOI 10.1038/s41586-020-2368-8