Figure legends:
Figure 1
Structure of the N-terminal domain
1a. Schematic of limited proteolysis data showing major (arrow) and minor tryptizination sites (line) in full length IBV nucleocapsid protein. The position of the N-terminal and C-termiinal domains are indicated by black rectangles.1b. Cartoon ribbon representation of the 1.3 Å structure of the N-terminal domain asymmetric homodimer (left) and dimer solved by Hui Fan et al (right) .1c. Hybrid, ribbon and surface representation of N-terminal domain with surface colored by electrostatic potential. The basic tethers are indicated by arrows.
Figure 2
Structure of the C-terminal domain
Stereo diagram of domain swapped C-terminal dimer. The asymmetric unit at pH 4.5 contains the dimer made up of two non-crystallographic symmetry related monomers shown in magenta and yellow. Butterfly shaped C-terminal dimer showing the anti-parallel β-sheet floor (top) and dimer turned through 90◦ with secondary structure elements numbered.
Figure 3
Interdimer interactions in C-terminal domain and structural conservation with related corona-like virus
3a. The asymmetric unit of the C-terminal domain crystallized at pH 8.5 with 8 molecules in the asymmetric unit (4 dimers each shown in a different color numbered 1 through 4). The two classes of dimer-dimer interactions arre indicated by T1 and T2. 3b. Crystal packing interactions in the pH 4.5 structure revealed by 3 consecutive dimers from neighboring asymmetric units (numbered n, n+1 and n-1). The monomers are colored differently and their N and C termini indicated( for thee middle dimer) . Salt bridge mediating dimer-dimer interactions in both spacegroups (inset and 3b right top and bottom). The various dimers from both spacegroups superimposed (3b right top) with each dimer in a different color. The dimer number 4 from pH 8.5 structure is colored yellow. A circle indicates the position of the common salt bridge seen in all dimer-dimer interactions.3c. Fold and quaternary structural similarity between IBV nucleocapsid protein N-terminal domain (3c left top) and PRRSV capsid forming domain (3c left bottom). The α-helices are colored red and the β-strands are colored yellow. 3 consecutive domain swapped dimers of PRRSV representing crystal packing interactions seen in PRRSV with conserved salt bridge (circled) are shown (3c right).
Figure 4
Linear fibre formation in C-terminal domain and N-terminal domain. Model for helical nucleocapsid formation.
4a. Electrostatic potential colored surface representation of head to tail N-terminal domain dimer-dimer interactions. Three consecutive asymmetric units are shown. N-terminal dimers with C-terminal loop interacting with groove on neighboring dimer (arrow). 90◦ view with disordered loops shown as dotted lines (4a right). 4b. Electrostatic potential colored surface of C-terminal domain at similar scale showing the compact c-terminal domain fibre with basic patches indicated by arrows. 4c Model for helical nucleocapsid formation as inferred from protein-protein interactions in structures of N-terminal and c-terminal domain. The C-terminal dimers are shown as red and green schematics with the exception of molecule 4 in pH 8.5 structure shown in black (4c inside dashed circle). The N-terminal had-to tail dimers are shown as black (this study) or red spheres ( study by Hui Fan et. al.). ssRNA genome is represented by a black curved-line.
Figure 5
Structure sequence relationships among dimerization domains of representative coronaviruses.
The sequences for 11 representative coronaviruses are shown with conserved residues indicated in red. The predicted secondary structure for SARS C-terminal domain (249-380) is superimposed on observed secondary structure for IBV C-terminal domain shown in red helices green strands and bluw loop regions. The residues involved in dimer-dimer interactions are shaded with purple boxes (dimer-dimer interactions type I, pH 4.5 and 8.5 ) or underlined with dark blue lines(dimer-dimer interactions of type II pH 8.5). The surface accessibility if indicated by a bar at bottom color coded totally accessible (white) to buried (dark blue) with experimental residue B-factors indicated on a scale from low (“b” text) to high (“B” text)