COVID-19 AlphaFold2 Models

From Proteopedia

Revision as of 15:02, 4 February 2022

spinqualitylabelsall models SARS-CoV-2 Protein N Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image 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 the SARS CoV-2 Protein N (UniProt ID: QHD43423) 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]. At present a number of proteins of the SARS CoV-2 virus have still not been experimentally determined. AlphaFold2 was used to predict 3D models for these proteins using the MIT ColabFold server[1] . For each prediction, five 3D models were predicted, ranked 1 to 5 (with 1 being the best). An example of such a predicted structure is the SARS CoV-2 Protein N (UniProt ID: QHD43423) color coded by the pLDDT scores. Views of these AlphaFold2 predictions can be seen on the following Proteopedia pages: SARS-CoV-2 protein M - Component of the viral envelope that plays a central role in virus morphogenesis and assembly via its interactions with other viral proteins.Cite error: Invalid <ref> tag; invalid names, e.g. too many[2]. SARS-CoV-2 protein N - The primary function of the Nucleocapsid protein (N-protein) is to package the viral genome into a helical ribonucleoprotein (RNP) complex[3][4]]

References

1. ↑ ^{1.0 1.1} MIT ColabFold https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/beta/AlphaFold2_advanced.ipynb
2. ↑ Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. J Proteome Res. 2020 Apr 3;19(4):1351-1360. doi: 10.1021/acs.jproteome.0c00129., Epub 2020 Mar 24. PMID:32200634 doi:http://dx.doi.org/10.1021/acs.jproteome.0c00129
3. ↑ <ref>. [[SARS-CoV-2 protein ORF10]] - It is currently unclear whether this region translates into a functional protein.<ref name="Zhang_Lab"></li> <li id="cite_note-3">[[#cite_ref-3|↑]] Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. J Proteome Res. 2020 Apr 3;19(4):1351-1360. doi: 10.1021/acs.jproteome.0c00129., Epub 2020 Mar 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/32200634 32200634] doi:[http://dx.doi.org/10.1021/acs.jproteome.0c00129 http://dx.doi.org/10.1021/acs.jproteome.0c00129]</li></ol></ref>