2025Li validation

Citation

Li, D., Perez, M.M., Zhang, X., Li, J. and Jiang, W. 2025. Validation of helical symmetry parameters in EMDB. Acta Crystallographica Sec. D. 81, (2025), 527–534.

Abstract

Helical symmetry is a structural feature of many biological assemblies, including cytoskeletons, viruses and pathological amyloid fibrils. The helical parameters twist and rise are unique metadata for helical structures. With the increasing number of helical structures being resolved through cryo-EM and deposited in the EMDB, there is a growing possibility of errors in the metadata associated with these entries. During our cryo-EM analysis of protein amyloids and the development of helical analysis tools, we realized that many deposited helical parameters appear to be inconsistent with the associated density maps. Here, we have developed a comprehensive validation process that examines the consistency of these parameters by combining high-throughput computational evaluation with manual verification. Multiple errors were identified and corrected for ~14% of the total entries, including missing parameters, swapped twist and rise values, incorrect sign of twist angles, partial symmetries and bona fide errors. Our validation code, workflow and the validated parameters are publicly available.

Links

https://journals.iucr.org/d/issues/2025/10/00/ni5031/index.html