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 Two of the structures were soon superseded by new higher-resolution data, confirming our proposed changes.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.

中文翻译：

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改善 SARS-CoV-2 结构：通过早期协调发布进行同行评审

这项工作建立在 SARS-CoV-2 蛋白和复合物的新实验 3D 结构破纪录的速度和大量立即发布的基础上，这对于下游疫苗和药物的开发至关重要。我们对这些结构进行了调查，以发现偶尔出现的错误，这些错误可能对这些重要用途很重要，并且我们能够提供明显更高精度的校正。该过程依赖于 CaBLAM 和 ISOLDE 等新的验证和校正方法，但尚未常规使用。我们在 7 个早期 SARS-CoV-2 结构中发现了如此重要且可纠正的问题。其中两个结构很快被新的更高分辨率的数据取代，证实了我们提出的更改。对于其他五个，我们通过电子邮件向存款人发送了一份有记录和插图的报告，并鼓励他们自己进行模型修正，并使用全球蛋白质数据库中的新选项，让存款人在不更改 PDB 代码的情况下重新版本其坐标。这样，即使在正式发布之前，任何检查或下载其结构的人都可以快速轻松地获得更准确的坐标。这些变化涉及序列错位、结合抑制剂附近不正确的RNA构象、不正确的金属配体以及阻碍相互作用位点良好接触的顺反或肽翻转。这些改进已经传播到后来完成的几乎所有相关结构中。这个过程构成了一种新形式的高度严格的同行评审，实际上比标准的出版物评审更快、更严格，因为它可以访问坐标和地图；期刊同行评审也将通过这种访问得到加强。