Table 1.
SARS‐CoV‐2 minimal models used in Fig 1.
| Statea | 3D Model | Identityb | Eb | Sourcec |
|---|---|---|---|---|
| NSP1 (NTR) | https://aquaria.ws/P0DTC1/7k3n | 100% | – | SARS‐CoV‐2 (Semper et al, 2021) |
| NSP1 (CTR) hijacks 40S, 43S, and 80S | https://aquaria.ws/P0DTC1/6zlw | 100% | – | SARS‐CoV‐2 (Thoms et al, 2020) |
| NSP3 (Ubl1) | https://aquaria.ws/P0DTC1/2gri | 77% | 10–21 | SARS‐CoV (Serrano et al, 2007) |
| NSP3 (macro) | https://aquaria.ws/P0DTC1/6woj | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6WOJ/pdb) |
| NSP3 (macro) mimics GDAP2 | https://aquaria.ws/P0DTC1/4uml | 20% | 10–15 | Human (https://doi.org/10.2210/pdb4UML/pdb) |
| NSP3 (macro) mimics MACROD1 | https://aquaria.ws/P0DTC1/2x47 | 27% | 10–160 | Human (Chen et al, 2011) |
| NSP3 (macro) mimics MACROD2 | https://aquaria.ws/P0DTC1/4iqy | 28% | 10–16 | Human (Jankevicius et al, 2013) |
| NSP3 (macro) mimics MACROH2A1 | https://aquaria.ws/P0DTC1/1zr5 | 19% | 10–13 | Human (Kustatscher et al, 2005) |
| NSP3 (macro) mimics MACROH2A2 | https://aquaria.ws/P0DTC1/2xd7 | 18% | 10–12 | Human (https://doi.org/10.2210/pdb2XD7/pdb) |
| NSP3 (macro) mimics PARP9 | https://aquaria.ws/P0DTC1/5ail | 23% | 10–10 | Human (https://doi.org/10.2210/pdb5AIL/pdb) |
| NSP3 (macro) mimics PARP14 | https://aquaria.ws/P0DTC1/3q6z | 29% | 10–12 | Human (Forst et al, 2013) |
| NSP3 (SUD‐N) + PAIP1 | https://aquaria.ws/P0DTC1/6yxj | 69% | 10–21 | SARS‐CoV (https://doi.org/10.2210/pdb6XYJ/pdb) |
| NSP3 (SUD‐M) | https://aquaria.ws/P0DTC1/2jzd | 80% | 10–23 | SARS‐CoV (Chatterjee et al, 2009) |
| NSP3 (SUD‐C) | https://aquaria.ws/P0DTC1/2kqw | 78% | 10–34 | SARS‐CoV (Johnson et al, 2010a) |
| NSP3 (PL‐Pro) | https://aquaria.ws/P0DTC1/6wrh | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6WRH/pdb) |
| NSP3 (PL‐Pro) hijacks ISG15 | https://aquaria.ws/P0DTC1/6xa9 | 100% | – | SARS‐CoV‐2 (Klemm et al, 2020) |
| NSP3 (PL‐Pro) hijacks UBA52 | https://aquaria.ws/P0DTC1/4rf0 | 31% | 10–31 | MERS‐CoV (Bailey‐Elkin et al, 2014) |
| NSP3 (PL‐Pro) hijacks UBB | https://aquaria.ws/P0DTC1/4wur | 30% | 10–30 | MERS‐CoV (Lei & Hilgenfeld, 2016) |
| NSP3 (PL‐Pro) hijacks UBC | https://aquaria.ws/P0DTC1/4mm3 | 83% | 10–30 | SARS‐CoV (Ratia et al, 2014) |
| NSP3 (PL‐Pro) hijacks UBB + UBC | https://aquaria.ws/P0DTC1/5e6j | 82% | 10–30 | SARS‐CoV (Békés et al, 2016) |
| NSP3 (PL‐Pro) binds inhibitory peptides | https://aquaria.ws/P0DTC1/6wuu | 99% | – | SARS‐CoV‐2 (Rut et al, 2020) |
| NSP3 (NAB) | https://aquaria.ws/P0DTC1/2k87 | 82% | 10–19 | SARS‐CoV (Serrano et al, 2009) |
| NSP4 | https://aquaria.ws/P0DTC1/3vcb | 59% | 10–37 | MHV‐A59 (Xu et al, 2009) |
| NSP4 binds NSP5 | https://aquaria.ws/P0DTC1/7kvg/C | 99% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb7KVG/pdb) |
| NSP5 (3CL‐Pro) | https://aquaria.ws/P0DTC1/5rfa | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb5RFA/pdb) |
| NSP5 binds inhibitory peptides | https://aquaria.ws/P0DTC1/7bqy | 100% | – | SARS‐CoV‐2 (Jin et al, 2020) |
| NSP7 | https://aquaria.ws/P0DTC1/2kys | 98% | 10–33 | SARS‐CoV (Johnson et al, 2010b) |
| NSP7 binds HLA | https://aquaria.ws/P0DTC1/7lg3 | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb7LG3/pdb) |
| NSP7 binds NSP8 | https://aquaria.ws/P0DTC1/6m5i/A | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6M5I/pdb) |
| NSP7 binds NSP8 + NSP12 | https://aquaria.ws/P0DTC1/6m71/C | 100% | – | SARS‐CoV‐2 (Gao et al, 2020) |
| NSP7 binds NSP8 + NSP12 + vRNA | https://aquaria.ws/P0DTC1/7aap/C | 100% | – | SARS‐CoV‐2 (Naydenova et al, 2021) |
| NSP7 binds NSP8 + NSP12 + vRNA + NSP13 | https://aquaria.ws/P0DTC1/6xez/C | 95% | – | SARS‐CoV‐2 (Chen et al, 2020) |
| NSP7 binds NSP8 + NSP12 + vRNA + NSP13 + NSP9 | https://aquaria.ws/P0DTC1/7cyq/C | 100% | – | SARS‐CoV‐2 (Yan et al, 2021a) |
| NSP8 | https://aquaria.ws/P0DTC1/6m5i/B | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6M5I/pdb) |
| NSP8 binds NSP12 | https://aquaria.ws/P0DTC1/6nus/B | 97% | 10–76 | SARS‐CoV (Kirchdoerfer & Ward, 2019) |
| NSP8 binds HLA | https://aquaria.ws/P0DTC1/7lg2 | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb7LG2/pdb) |
| NSP9 | https://aquaria.ws/P0DTC1/6wxd | 98% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6WXD/pdb) |
| NSP10 | https://aquaria.ws/P0DTC1/2g9t | 96% | 10–72 | SARS‐CoV (Su et al, 2006) |
| NSP10 binds NSP14 | https://aquaria.ws/P0DTC1/5c8u/A | 95% | 10–68 | SARS‐CoV (Ma et al, 2015) |
| NSP10 binds NSP16 | https://aquaria.ws/P0DTC1/6w61/B | 99% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6W61/pdb) |
| NSP12 | https://aquaria.ws/P0DTD1/6yyt | 100% | – | SARS‐CoV‐2 (Hillen et al, 2020) |
| NSP12 binds vRNA | https://aquaria.ws/P0DTD1/3koa | 15% | 10–14 | FMDV (Ferrer‐Orta et al, 2010) |
| NSP13 | https://aquaria.ws/P0DTD1/6jyt | 100% | 10–63 | SARS‐CoV (Jia et al, 2019) |
| NSP13 mimics AQR | https://aquaria.ws/P0DTD1/4pj3 | 20% | 10–27 | Human (De et al, 2015) |
| NSP13 mimics AQR + spliceosome | https://aquaria.ws/P0DTD1/6id0 | 20% | 10–27 | Human (Zhang et al, 2019) |
| NSP13 mimics UPF1 | https://aquaria.ws/P0DTD1/2wjy | 24% | 10–53 | Human (Clerici et al, 2009) |
| NSP13 mimics UPF1 + UPF2 | https://aquaria.ws/P0DTD1/2wjv | 24% | 10–53 | Human (Clerici et al, 2009) |
| NSP13 mimics IGHMBP2 | https://aquaria.ws/P0DTD1/4b3f | 25% | 10–32 | Human (Lim et al, 2012) |
| NSP13 mimics IGHMBP2 + hRNA | https://aquaria.ws/P0DTD1/4b3g | 26% | 10–31 | Human (Lim et al, 2012) |
| NSP13 binds vRNA | https://aquaria.ws/P0DTD1/4n0o | 21% | 10–19 | Arterivirus (Deng et al, 2014) |
| NSP13 binds HLA | https://aquaria.ws/P0DTD1/7lfz | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb7LFZ/pdb) |
| NSP14 | https://aquaria.ws/P0DTD1/5nfy | 95% | 10–142 | SARS‐CoV (Ferron et al, 2018) |
| NSP15 | https://aquaria.ws/P0DTD1/6wxc | 97% | – | SARS‐CoV‐2 (Kim et al, 2021) |
| NSP15 binds vRNA | https://aquaria.ws/P0DTD1/6x1b | 97% | – | SARS‐CoV‐2 (Kim et al, 2021) |
| NSP16 | https://aquaria.ws/P0DTD1/6w4h | 99% | – | SARS‐CoV‐2 (Rosas‐Lemus et al, 2020) |
| NSP16 mimics CMTR1 | https://aquaria.ws/P0DTD1/4n49 | 14% | 10–11 | Human (Smietanski et al, 2014) |
| NSP16 mimics MRM2 | https://aquaria.ws/P0DTD1/2nyu | 22% | 10–11 | Human (https://doi.org/10.2210/pdb2NYU/pdb) |
| NSP16 mimics CMTR1 + hRNA | https://aquaria.ws/P0DTD1/4n48 | 14% | 10–11 | Human (Smietanski et al, 2014 |
| NSP16 binds vRNA + NSP10 | https://aquaria.ws/P0DTD1/7jyy/A | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb7JYY/pdb) |
| Spike glycoprotein | https://aquaria.ws/P0DTC2/6vxx | 97% | – | SARS‐CoV‐2 (Walls et al, 2020) |
| Spike glycoprotein hijacks ACE2 | https://aquaria.ws/P0DTC2/7ct5 | 100% | – | SARS‐CoV‐2 (Guo et al, 2021) |
| Spike glycoprotein hijacks ACE2 + SLC6A19 | https://aquaria.ws/P0DTC2/6m17 | 100% | – | SARS‐CoV‐2 (Yan et al, 2020) |
| Spike glycoprotein hijacks NRP1 | https://aquaria.ws/P0DTC2/7jjc | 100% | – | SARS‐CoV‐2 (Daly et al, 2020) |
| Spike glycoprotein binds antibodies | https://aquaria.ws/P0DTC2/6w41 | 100% | – | SARS‐CoV‐2 (Yuan et al, 2020a) |
| Spike glycoprotein binds inhibitory peptides | https://aquaria.ws/P0DTC2/5zvm | 88% | 10–33 | SARS‐CoV (Xia et al, 2019) |
| ORF3a | https://aquaria.ws/P0DTC3/6xdc | 100% | – | SARS‐CoV‐2 (preprint: Kern et al, 2020) |
| ORF3a binds APOA1 | https://aquaria.ws/P0DTC3/7kjr | 100% | – | SARS‐CoV‐2 (preprint: Kern et al, 2020) |
| Envelope protein | https://aquaria.ws/P0DTC4/5x29 | 85% | 10–35 | SARS‐CoV (Surya et al, 2018) |
| Envelope protein hijacks MPP5 | https://aquaria.ws/P0DTC4/7m4r | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb7M4R/pdb) |
| ORF7a | https://aquaria.ws/P0DTC7/6w37 | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6W37/pdb) |
| ORF8 | https://aquaria.ws/P0DTC8/7jtl | 99% | – | SARS‐CoV‐2 (Flower et al, 2021) |
| Nucleocapsid protein (NTD) | https://aquaria.ws/P0DTC9/6yi3 | 96% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6YI3/pdb) |
| Nucleocapsid protein (NTD) binds antibody | https://aquaria.ws/P0DTC9/7cr5 | 100% | – | SARS‐CoV‐2 (Daly et al, 2020) |
| Nucleocapsid protein (NTD) binds HLA | https://aquaria.ws/P0DTC9/7kgr | 100% | – | SARS‐CoV‐2 (Szeto et al, 2021) |
| Nucleocapsid protein (NTD) binds vRNA | https://aquaria.ws/P0DTC9/7acs | 96% | – | SARS‐CoV‐2 (Dinesh et al, 2020) |
| Nucleocapsid protein (CTD) | https://aquaria.ws/P0DTC9/6yun | 98% | – | SARS‐CoV‐2 (Zinzula et al, 2021) |
| Nucleocapsid protein (CTD) binds HLA | https://aquaria.ws/P0DTC9/7kgo | 100% | – | SARS‐CoV‐2 (Szeto et al, 2021) |
| ORF9b | https://aquaria.ws/P0DTD2/6z4u | 100% | – | SARS‐CoV‐2 (https://doi.org/10.2210/pdb6Z4U/pdb) |
| ORF9b hijacks TOMM7 | https://aquaria.ws/P0DTD2/7kdt | 100% | – | SARS‐CoV‐2 (Gordon et al, 2020) |
a
This table lists 79 distinct protein structural states found in this work, each with details on one representative minimal model, indicated using an Aquaria identifier. The indicated models correspond to those used to generate representative images and hyperlinks in the online version of Fig 1.
b
In cases showing potential mimicry, the identity scores and E‐values indicate similarity between the SARS‐CoV‐2 viral protein and a human protein.
c
Indicates the organism used to derive the corresponding PDB structure as well as the publication associated with the PDB entry; where no publication is yet available, the DOI for the dataset is given. Organism names are abbreviated as follows: FMDV (foot‐and‐mouth disease virus); MERS‐CoV (Middle East respiratory syndrome coronavirus); MHV‐A59 (mouse hepatitis virus A59); SARS‐CoV (severe acute respiratory syndrome coronavirus); SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus 2).