[3dem] An urgent appeal to the community to deposit COVID-19-related cryo-EM raw data to EMPIAR

[Ardan Patwardhan]

Dear all,

Structural biology is playing a vital role in COVID-19 research and the race to develop therapeutics and vaccines. As a result we have seen a large number of SARS-CoV-2 structures being determined very rapidly and deposited in PDB and EMDB. 

However, it is important to keep in mind that most biologists and bioinformaticians use models deposited to the PDB without much (if any) consideration of how well these are supported by the experimental data (this is true for X-ray and cryo-EM). 

In the rush to get structures out it is to be expected that mistakes are sometimes made and structures are perhaps pushed out without receiving the scrutiny they would typically get. Unfortunately, there are potentially severe implications if the modelling is wrong in critical regions like the binding sites.

If the raw data underlying these structures were to be made publicly available, the cryo-EM community could contribute to the global effort by reprocessing and reanalysing these data. Just think about the number of times the β-galactosidase dataset (https://www.ebi.ac.uk/pdbe/emdb/empiar/reuse <https://www.ebi.ac.uk/pdbe/emdb/empiar/reuse>; https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10061/ <https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10061/>) has been reanalysed!

This is especially pertinent given the global implications of the current health crisis and the urgent need for diagnostics, drugs and vaccines. We expect that many cryo-EM researchers will be motivated to contribute, at a time when they find themseves at home and often unable to collect any new data themselves.

We would therefore like to make the following urgent appeal:

a) if you have deposited any cryo-EM structures related to SARS-CoV-2 to EMDB (and possibly PDB), please deposit the raw data to EMPIAR.

b) if you have collected cryo-EM data related to SARS-CoV-2 but not yet deposited a structure, please consider depositing the raw data to EMPIAR so that the processing and model-building can be crowd-sourced.

Once raw data is available in EMPIAR we will announce this through the cryo-EM mailing lists and Twitter so that anybody can take these data and (re)process them. The resulting maps (and models) can in turn be deposited to EMDB/PDB, so that people with expertise in model building and validation can also bring their skills to bear to try and improve on the models.

Although all EMBL-EBI staff are working remotely, EMPIAR is fully up and running both for depositing and downloading data.
For depositors and users from Japan, South Korea and China, we recommend depositing/downloading via EMPIAR-Japan (see link below).

Relevant URLs:

- EMPIAR website: https://empiar.org/ <https://empiar.org/>

- EMPIAR deposition system: https://www.ebi.ac.uk/pdbe/emdb/empiar/ <https://www.ebi.ac.uk/pdbe/emdb/empiar/>

- EMPIAR policies and processing procedures: https://www.ebi.ac.uk/pdbe/emdb/empiar/policies <https://www.ebi.ac.uk/pdbe/emdb/empiar/policies>

- EMPIAR mirror site in Japan: https://empiar.pdbj.org/ <https://empiar.pdbj.org/>

If you require any assistance, please contact the EMPIAR helpdesk: empiar-help at ebi.ac.uk <mailto:empiar-help at ebi.ac.uk>

Many thanks and stay safe!

Ardan Patwardhan & Gerard Kleywegt (EMBL-EBI); Genji Kurisu (Osaka University)
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