puzzle picture
1844: Coronavirus ORF3a Prediction
Status: Closed

Summary

Name: 1844: Coronavirus ORF3a Prediction
Status: Closed
Created: 05/28/2020
Points: 100
Expired: 06/04/2020 - 23:00
Difficulty: Intermediate
Description: 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!

Sequence:
WKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL
Categories: Overall, Prediction

Top Groups

RankGroupScorePoints
1Go Science11,451100
2Gargleblasters10,95680
3Anthropic Dreams10,92863
4Team India10,61049
5Hold My Beer10,48437

Top Evolvers

Top Soloists



Need this puzzle? Log in to download.  

Comments

bkoep's picture
User offline. Last seen 4 hours 31 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
PSIPRED Predictions

Conf: 962248952023898999555885446656789996999839985466210130014604
Pred: CCCCCCCCCCCCCCEEEEEECCCCCEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCEE
  AA: WKCRSKNPLLYDANYFLCWHTNCYDYCIPYNSVTSSIVITSGDGTTSPISEHDYQIGGYT
              10        20        30        40        50        60


Conf: 113344213899998535773786403210278740588898554368925430788941
Pred: EECCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCEEEEEEEEECCCCCHHCEEEEEEE
  AA: EKWESGVKDCVVLHSYFTSDYYQLYSTQLSTDTGVEHVTFFIYNKIVDEPEEHVQIHTID
              70        80        90       100       110       120


Conf: 7988336877533478984002479
Pred: CCCCCCCCCCCCCCCCCCCCCCCCC
  AA: GSSGVVNPVMEPIYDEPTTTTSVPL
             130       140
Joined: 01/19/2019
Groups: Go Science
Routine information

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.

User login
Download links:
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.12 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Social Media


Search
Only search fold.it
Other Games: Mozak
Recommend Foldit
Topics
Top New Users
Sitemap

Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons