SARS-CoV-2 protein NSP11

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Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.
Model Confidence:

  Very high (pLDDT > 90)

  Confident (90 > pLDDT > 70)

  Low (70 > pLDDT > 50)

  Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be unstructured in isolation.

To the right is an AlphaFold2 3D model of SARS CoV-2 Protein NSP11 (length = 13 amino acids, i.e. SADAQSFLNGFAV color coded by the pLDDT scores. It corresponds to the highest ranked model in terms of the pLDDT confidence scores, i.e., model 5[1].

Morph of the top 5 ranked AlphaFold2 models of SARS-CoV-2 Protein NSP11, rainbow color coded N-C (blue to red).
Morph of the top 5 ranked AlphaFold2 models of SARS-CoV-2 Protein NSP11, rainbow color coded N-C (blue to red)[1].


Function

Non-structural protein 11 (NSP11) is the short peptide at the C-term of the large SARS-CoV-2 polyprotein ORF1ab (pp1a). it is the cleavage product of pp1a polyprotein by 3CLpro/Mpro protease at the nsp10/11 junction. NSP11 overlaps a portion of the RNA that codes for NSP12, so whether NSP11 is actually expressed as well as its putative function is not known[2].


Structural Highlights

Giri's lab[3] studied NSP11 in solution and by molecular dynamics. Based on CD, they found that NSP11 shows characteristics of an intrinsically disordered protein (IDP). They further studied the its conformational behavior in the presence of negatively charged and neutral liposomes, and found that it remains disordered. However, in SDS micelle, NSP11 adopts an α-helical conformation, suggesting the helical propensity of NSP11, which is very similar to what [AlphaFold[2 predicts. Based on MD simulations NSP11 appears to to have the behavior of an IDP.

See also

Coronavirus_Disease 2019 (COVID-19)
SARS-CoV-2_virus_proteins
COVID-19 AlphaFold2 Models


AlphaFold2 model of NSP11 (Rank1, Model 5)
Drag the structure with the mouse to rotate

References

  1. ↑ 1.0 1.1 MIT ColabFold
  2. ↑ NY Times (3-Apr-2020) Bad News Wrapped in Protein: Inside the Coronavirus Genome
  3. ↑ Gadhave K, Kumar P, Kumar A, Bhardwaj T, Garg N, Giri R. Conformational dynamics of 13 amino acids long NSP11 of SARS-CoV-2 under membrane mimetics and different solvent conditions. Microb Pathog. 2021 Sep;158:105041. doi: 10.1016/j.micpath.2021.105041. Epub 2021, Jun 10. PMID:34119626 doi:http://dx.doi.org/10.1016/j.micpath.2021.105041

Proteopedia Page Contributors and Editors (what is this?)

Joel L. Sussman

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