When two into one won't go: fitting in the presence of steric hindrance and partial occupancy.
Combining structural data from cryo-electron microscopy (cryo-EM) and X-ray crystallography to give pseudo-atomic models of large molecular complexes has proved particularly suitable for studying viruses and viral complexes. Several groups are developing programs to fit X-ray data to EM data. These programs are in general tailored to particular problems with regard to size, symmetry, number of rigid bodies, resolution etc. Here, two approaches are described to fitting X-ray data to EM data in the presence of steric interference and their relative merits and limitations are indicated. These fitting techniques are applied to the case of the rotavirus double-layered particle (DLP) in complex with antibodies which inhibit the transcription of mRNA by the DLP. This is a particularly good test case, as the cryo-electron microscopy map of the DLP-Fab complex, the X-ray structure of the viral protein (VP6) and also that of the VP6-Fab complex are available. The estimation of partial occupancy is also considered.
Thouvenin
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Institut de Biologie Structurale J.-P. Ebel, 42 Rue Jules Horowitz, 38027 Grenoble, France.
Hewat
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D000818:Animals; D000914:Antibodies, Viral / Q000737:chemistry* / Q000648:ultrastructure; D000956:Antigens, Viral; D001666:Binding Sites, Antibody; D002213:Capsid / Q000737:chemistry / Q000648:ultrastructure; D036022:Capsid Proteins; D020285:Cryoelectron Microscopy / Q000379:methods; D018360:Crystallography, X-Ray / Q000379:methods; D017929:Hemorrhagic Disease Virus, Rabbit / Q000648:ultrastructure*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D012333:RNA, Messenger / Q000235:genetics; D011817:Rabbits; D012401:Rotavirus / Q000276:immunology / Q000648:ultrastructure*; D014158:Transcription, Genetic
D000914:Antibodies, Viral; D000956:Antigens, Viral; D036022:Capsid Proteins; D007140:Immunoglobulin Fab Fragments; D012333:RNA, Messenger; C061332:VP6 protein, Rotavirus