Making the invisible enemy visible

Abstract

Structural biology plays a crucial role in the fight against COVID-19, permitting us to ‘see’ and understand SARS-CoV-2. However, the macromolecular structures of SARS-CoV-2 proteins that were solved with great speed and urgency can contain errors that may hinder drug design. The Coronavirus Structural Task Force has been working behind the scenes to evaluate and improve these structures, making the results freely available at https://insidecorona.net/.

Fig. 1 |. Examples of common errors and improvements.

All pictures except i are screenshots from the Coot v0.9.9 prerelease. Residual density and reconstruction maps are in blue-gray, difference electron density in red and green. a, SARS-CoV-1 Nsp14–Nsp10 (PDB 5C8T) histidine zinc-coordination site (B603), with residual density contour level 0.445, root mean square deviation (r.m.s.d.) 0.150. b, Histidine from a has been swapped in ISOLDE, leading to tetrahedral coordination of Zn²⁺, then refinement was performed using PDB-REDO with manual addition of links. c, Proline A505 is modelled as trans in the RdRp complex (PDB 7BV2, left), but the density indicates a cis main chain conformation, shown in d. d, The deposited PDB entry was updated after we contacted the original authors. e, High difference electron density at residue A165 in the SARS-CoV-2 main protease (PDB 5RFA) due to an occupancy of only 0.44 rather than 1.00 near the potential inhibitor (left). Residual map contour level 0.54, r.m.s.d. 0.319; difference density at contour level 0.35, r.m.s.d. 0.114. f, SARS-CoV-2 spike receptor-binding domain complexed with human ACE2 (PDB 6VW1). This N-linked glycan is flipped approximately 180° around the N-glycosidic bond. After we contacted the original authors, this entry was revised (shown in g). g, Correction improves the density fit of the sugar chain. Residual map at contour level 0.311, r.m.s.d. 0.265. h, Disulfide bond A226–A189 in papain-like protease (PDB 6W9C), with electron density at contour level 0.214, r.m.s.d. 0.136; the other two cysteine residues remain uncoordinated. While the density map does not indicate a zinc, it is a zinc finger domain; the other NCS copies include a coordinated zinc at this position. i, AUSPEX plot of SARS-CoV main protease (PDB 2HOB); ice rings are reflected by a bias in the intensity distribution (red). j, Ramachandran plot or torsion angles in the peptide backbone for the SARS-CoV Nsp10–Nsp14 dynamic complex (PDB 5NFy). In principle, there should only be a few outliers (red), as most peptide bonds adhere to typical angular distributions. Picture: CSTF/insidecorona.net.

Fig. 2 |. Register shift in the c terminus of rNa polymerase.

a, Overview with missing loop shown as a dashed line (PDB 7BV2); map at 2.4σ. Right, details of the C-terminal helix at 5σ. b, Lower resolution map and model (PDB 6NUS). Judging the side chain fit is difficult. c, Higher resolution map and model (PDB 7BV2) as deposited; the side chain fit is suboptimal due to the register error. d, Amended model for PDB 7BV2; the side chains now fit the density. The register shift is indicated by the labelled Tyr915. Picture: CSTF/insidecorona.net.