Fold this coronavirus protein! This is a portion of a larger protein encoded in the viral genome of SARS-CoV-2. It is encoded in a region of the genome called ORF3a, but the protein's structure and function are still unknown. If we knew how this protein folds, we might be able to figure out its exact function. The puzzle's starting structure shows SS predictions from PSIPRED, and hints which parts of the protein might fold into helices or sheets. Refold this protein to find high-scoring solutions, which will tell us how this protein is most likely to fold!
This is presumably the cytoplasmic part of ORF3a (UniProt P59632 for the very similar SARS-Cov-1 version). In line with this environment, no disulfides are expected by DiaNNA.
This thing is somewhat conserved in other betacov genomes; bat versions include A0A088DI21 and A0A1B3Q5V5. Below is an alignment of these guys; you can see the human-infecting SARSr-COVs have some extensions not found in the two bat versions.
>Pz1844
WKCRSKNPLLYDANYFLCWHTN
CYDYCIPYNSVTSSI-VITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDY
YQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTCT
SVP-
>New|UniRef100_A0A088DI21 Uncharacterized protein n=1 Tax=Bat Hp-betacoronavirus/Zhejiang2013 TaxID=1541205 RepID=A0A088DI21_9BETC
IRCKSLVPLCADDDCFVNYNAG
GKTYCMPFDPNEPYLTLVVHQNGIT---------CGSYKLYGDVSIADRIYLVTLTKSVP
YSLQNI---FDAELCTIAFYIADCAV------IEDHTTAGKTPRLELKSDPIYEVPCATI
DVPL
>New|UniRef100_A0A1B3Q5V5 NS3 protein n=1 Tax=Rousettus bat coronavirus TaxID=1892416 RepID=A0A1B3Q5V5_9BETC
IRVHSMAPFVSTADNFAVLRTT
CSRFVFPVESSKDNVVVLTTSRGVF---------CNGIHVEGPTALSDNASIVSLFSTTV
LLLDRVEQGYDY---TVFVYISQQILRNSE--------SNPQGVVNPEFD----------
DVEL
This probably won't work, but just for the sake of fun I told Rosetta's GREMLIN to try and figure out what residues are changing together. This sort of correlation is usually indicative of close contact in the actual protein. http://openseq.org/sub.php?id=1591034373 The last time GREMLIN tried it was in 2013 without enough sequences to work with, and I don't really see that changing much: http://gremlin.bakerlab.org/pfam.php?id=PF11289&year=2013.
