Reconstruction of the Flexible IgM Fc Core Using Atomic Force Microscopy Topography and the AFM-Assembly Pipeline

Area of Science:

• Structural Biology
• Immunology
• Biophysics

Background:

• Immunoglobulin M (IgM) is a crucial antibody class initiating immune responses and regulating autoimmunity.
• Pentameric IgM comprises an Fc core (Cμ2, Cμ3, Cμ4 domains) and 10 Fab domains.

Purpose of the Study:

• To reconstruct a pseudo-atomic model of the pentameric IgM Fc core using high-resolution atomic force microscopy (AFM).
• To investigate the structural assembly and conformational flexibility of the IgM Fc core.

Main Methods:

• Utilized high-resolution AFM topography to constrain the reconstruction of the pentameric IgM Fc core.
• Employed the AFM-Assembly pipeline, including DockAFM, to fit known cryo-EM and X-ray structures.
• Integrated structural units to generate a complete pentameric IgM Fc core model.

Main Results:

• The reconstruction revealed differential assembly of the five Cμ2 monomers.
• Monomers M1 and M5 exhibited tight attachment to the inner core, while M2-M4 were loosely bound.
• Multiple alternative conformations for Cμ2 domain attachment were identified, indicating molecular flexibility.

Conclusions:

• The study provides an experimentally constrained model of the pentameric IgM Fc core structure.
• The findings highlight the dynamic nature and conformational variability in IgM Fc assembly.
• The reconstruction protocol effectively integrates molecular flexibility observed in AFM studies.