Fig. 2
From: The 3.3 Å structure of a plant geminivirus using cryo-EM
Building a geminate capsid. a Rear half of the EM density for AYVV at 3.3 Å resolution. The cut surface of the EM density is colored bright magenta for clarity. Three CP subunits from each hemisphere are colored as in Fig. 1. In the top hemisphere, these are H-I-H (blue-maroon-blue) and in the bottom hemisphere these are I-H-I (colored maroon-blue-maroon). b Zoomed-in view of the interactions that form the interface. A helix-loop-helix motif comprising residues 40–63, becomes ordered only in subunit H (green halo), whilst an extra segment (residues 55–63) in subunit I also becomes ordered (orange halo) but in a different conformation to that seen by the same residues in chain H. c Details of the interactions across the equatorial interface. The loop in the helix-loop-helix motif makes H-bonding and van der Waals interactions with a patch of polar residues (214–215) on the opposing subunit. This patch is normally exposed on the surface of the subunits that form the isometric parts of the capsid (see Supplementary Fig. 4). d Details of the interaction between the two different N-terminal conformations. Effectively a beta-strand interaction is formed from backbone H-bonding of residues 59–61 in H (blue) and residues 56–59 in I, which helps to stabilize the ring of H & I subunits within a hemisphere
