Abstract:
:This work builds upon the record-breaking speed and generous immediate release of new experimental 3D structures of the SARS-CoV-2 proteins and complexes, which are crucial to downstream vaccine and drug development. We have surveyed those structures to catch the occasional errors that could be significant for those important uses and for which we were able to provide demonstrably higher-accuracy corrections. This process relied on new validation and correction methods such as CaBLAM and ISOLDE, not yet in routine use. We found such important and correctable problems in seven early SARS-CoV-2 structures. Two of the structures were soon superseded by new higher-resolution data, confirming our proposed changes. For the other five, we emailed the depositors a documented and illustrated report, and encouraged them to make the model corrections themselves and use the new option at the worldwide Protein Data Base for depositors to re-version their coordinates without changing the PDB code. This quickly and easily makes the better-accuracy coordinates available to anyone who examines or downloads their structure, even before formal publication. The changes have involved sequence misalignments, incorrect RNA conformations near a bound inhibitor, incorrect metal ligands, and cis-trans or peptide flips that prevent good contact at interaction sites. These improvements have propagated into nearly all related structures done afterward. This process constitutes a new form of highly rigorous peer review, which is actually faster and more strict than standard publication review, because it has access to coordinates and maps; journal peer review would also be strengthened by such access.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Croll TI,Williams CJ,Chen VB,Richardson DC,Richardson JSdoi
10.1016/j.bpj.2020.12.029subject
Has Abstractpub_date
2021-01-15 00:00:00eissn
0006-3495issn
1542-0086pii
S0006-3495(21)00046-1pub_type
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