Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy  Katharina Hipp, Clemens Grimm, Holger Jeske, Bettina Böttcher  Structure  Volume 25, Issue 8, Pages 1303-1309.e3 (August 2017) DOI: 10.1016/j.str.2017.06.013 Copyright © 2017 Elsevier Ltd Terms and Conditions

Structure 2017 25, 1303-1309.e3DOI: (10.1016/j.str.2017.06.013) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 1 Structure of ACMV Particles (A) Surface representation of the final EM map without B-factor sharpening. The structurally different capsomers are indicated. T, top capsomer with five-fold symmetry; S, shoulder capsomer with local five-fold symmetry; W, waist capsomer making contact with the other half of the particle. Scale bar, 10 nm. (B) Slice through the center of the EM map. Arrows indicate density below the capsomers that might originate from DNA. (C) CP structure modeled into the EM density map. (D) ACMV-K CP sequence with the major β-strands labeled and underlined. Structure 2017 25, 1303-1309.e3DOI: (10.1016/j.str.2017.06.013) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 2 CP Models Fit into the EM Density Map (A) Five CP models were fit into the EM density map at the position of the T capsomer and viewed from the outside of the particle. The FG-loops constitute the local and strict five-fold symmetry axes, and Y193 (shown with its side chain in the center of the capsomer; position also indicated in C) is forming the tip of these loops constituting the cap of the capsomer. (B) The inside of the capsomers at and close to the five-fold symmetry axes is lined with positively charged side chains (space-filled, blue) forming a plug (K196) and a two-layered ring (K202, R203). (C) The capsomer as in (B) is shown from the side with the front half cut away. The lysines and arginines are in close proximity to the density below the capsomers as described in Figure 1B. Additionally the positions of Y193 (red) and P63 (green) as the first N-terminally resolved residue in the modeled CP are indicated. Structure 2017 25, 1303-1309.e3DOI: (10.1016/j.str.2017.06.013) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 3 Inter-Capsomer Contacts The backbone of CPs interacting across capsomers are fit into the EM density and shown from the outside of the particle in rainbow colors from blue at the N terminus to cyan, green, yellow, and red at the C terminus; the β-strands are named as in Figure S2D. (A) The contact between two capsomers at the local two-fold symmetry axes are mediated by the EF- and GH-loops of both subunits. (B) At the local three-fold axes, CPs interact via their CD-loops (cyan) and to some extent with the GH-loop (yellow). (C and D) At the true two-fold symmetry axes, the contact is mediated either by four CPs from four different capsomers, two from each half particle (C), or by two CPs, one from either half of the particle (D) on the other end of the symmetry axes. (C) At the contact site including four capsomers, the N terminus of the CPWII subunits (N-terms, blue) as well as the GH- and CD-loops of the CPWI subunits (yellow and cyan, respectively) are involved in interaction. (D) Two capsomers at the particle waist interact via the EF-loops of both CPWI subunits. (E and F) A slice through the tip of two capsomers within one half of the particle (E) or across the particle waist (F) is shown. Capsomers within on half are connected with angle of 115°, whereas capsomers at the perimeter are joined concavely at −147°. Structure 2017 25, 1303-1309.e3DOI: (10.1016/j.str.2017.06.013) Copyright © 2017 Elsevier Ltd Terms and Conditions

Figure 4 Consequences for Insect Transmission (A) The CP model is shown from the side (left) or from the outside (right). Amino acid side chains implicated in insect transmission of several begomoviruses are highlighted (positions in the ACMV sequence): Q130 (yellow), N131 (green), Q156 (cyan), and L181 (blue). (B) A capsomer with the five CP models is shown along the five-fold symmetry axis from the outside of the particle (left) and from the side after rotation by 90° (right). The red subunit on the right panel is depicted in the same orientation as in right-hand panel of (A). The amino acid side chains described in (A) are selected with the same colors. Structure 2017 25, 1303-1309.e3DOI: (10.1016/j.str.2017.06.013) Copyright © 2017 Elsevier Ltd Terms and Conditions