Protein-complex structure completion usingIPCAS(Iterative Protein Crystal structure Automatic Solution)

Abstract

Protein complexes are essential components in many cellular processes. In this study, a procedure to determine the protein-complex structure from a partial molecular-replacement (MR) solution is demonstrated using a direct-method-aided dual-space iterative phasing and model-building program suite,IPCAS(Iterative Protein Crystal structure Automatic Solution). TheIPCASiteration procedure involves (i) real-space model building and refinement, (ii) direct-method-aided reciprocal-space phase refinement and (iii) phase improvement through density modification. The procedure has been tested with four protein complexes, including two previously unknown structures. It was possible to useIPCASto build the whole complex structure from one or less than one subunit once the molecular-replacement method was able to give a partial solution. In the most challenging case,IPCASwas able to extend to the full length starting from less than 30% of the complex structure, while conventional model-building procedures were unsuccessful.