Cryo-EM Structure Deposition


Once a protein structure is solved it is usually deposited in the World Wide Protein Data Bank (wwPDB). This is necessary for publication as most journals require a PDBID to be included in any manuscript under review that describes a new crystallographic structure. The wwPDB is an invaluable resource that contains many tens of thousands of structures, which are increasingly used to solve new crystal structures by molecular replacement.


The model files generated by phenix.real_space_refine contain information that is useful when depositing a structure to the wwPDB. However, a much better route is to deposit mmCIF format files, for the model. To get a mmCIF format file in the phenix.real_space_refine GUI, the process is similar to that in phenix.refine. In the "Output" section of the "Input/Output" panel, there is a check box labelled "Write final model in mmCIF." After the model is output, you can add the sequence to the file with the mmtbx.prepare_pdb_deposition program (from the command line). This program requires the full sequence for the macromolecule to be provided. The result of this will be a mmCIF file containing the model.

Common issues

Related programs