Table 1.
Data collection and refinement statistics of Safo-4PUS-pH4.7.
Figure 1.
Structure of truncated N1-165 domain of M1 (PDB code 4PUS) at pH 4.7.
A. Monomer A of 4PUS. The N-terminal and C-terminal domains are shown in grey ribbons. Shown in yellow sticks are the basic NLS motif residues (Arg101, Lys102, Lys104, Arg105), Lys95 and Lys98 located on the right face of the molecules; the negatively charged residues Glu8, Glu23, Glu29, Asp30, Asp38, and Glu44 located on the left face of the molecule; and representative hydrophobic core residues on H1 and H4 buried between the N-terminal and C-terminal domains. For clarity not all residues of interest are shown. The nine helices are labelled B. Dimeric structure showing the positively charged residues including the NLS (yellow sticks) on the surface of the molecule. Monomers A and B are colored in grey and orange, respectively. Note the disorder in the N-terminal domain of monomer B. C. Same as figure B, but rotated by ∼90°. D and E. Final refined 2Fo-Fc electron density maps (contoured at 0.9α) of analogous regions (residues 45–50) of monomers A and B, respectively. The region in monomer B is clearly disordered.
Table 2.
Hydrogen bond interactions (<3.8 Å) and solvent accessible buried surface area of the monomer–monomer interface of M1 structures.
Figure 2.
Comparison of 4PUS with other truncated N1-165 domain M1 structures (in ribbon diagrams).
Unless noted otherwise, monomers A and B are colored grey and orange, respectively. A. Superposition of monomers A of 4PUS (grey), 1AA7 (yellow), and 1EA3 (red). B. Dimeric structure of 1AA7 showing face-to-face interaction between the two monomers. C. Relative positions of the non-superposed monomers B of 4PUS (grey), 1AA7 (yellow) and 3MD2 (red) after superposition of the corresponding monomers A. For clarity, only parts of the non-superposed monomers B are shown. D. Two monomers of 1EA3 interacting in a face-to-back fashion with the positively charged residues facing the negatively charged residues. For clarity not all positive or negative residues at the monomer faces are shown.
Figure 3.
Packing (stacking) arrangement of the M1 molecules (in ribbon diagrams). Monomers A and B are colored grey and orange, respectively.
A. A dimer of 1AA7 stacked on top of another dimer to form a pseudo-tetramer. A similar arrangement is observed in 3MD2. B. A pseudo-tetramer appears to form similarly in 4PUS, however, the two stacked dimers do not interact with each other. C. Arrangement of monomers in 1EA3 to form a pseudo-tetramer.
Figure 4.
Schematic representation of the proposed multiple conformational transitions in M1 structures.
A. Cartoon diagrams illustrating the oligomeric state of the M1 crystal structures, including 4PUS (grey), 1AA7 (blue), 3MD2 (red), 1EA3 (magenta) and 2Z16 (yellowish-green). Structures at neutral pH (top) are monomeric and arranged face-to-back; those at acidic pH (bottom) are dimeric and arranged face-to-face. Disorder in the Safo (4PUS) structure is indicated by a light-colored region bounded by a dashed line. B. Cartoon illustrating the interfacial regions of 4PUS (grey), 1AA7 (blue), 3MD2 (red), 1EA3 (magenta) and 2Z16 (yellowish-green). Individual M1 chains (consisting of two four-helix bundles separated by a linker) are represented as rectangles. Each crystal structure is represented by an ‘A’ chain (leftmost rectangle; grey border) and a ‘B’ chain (rightmost rectangle). The acidic (red) and basic (blue) residues at the interfacial regions are labeled and may be grouped into five clusters (K21; E8, E29 and D30; R76, R77 and R78; D89, D94, K95, K98, R101 and K104; R134) based on their proximity to one another on the M1 surface. Salt bridges are represented by yellow rectangles joining opposite charges. Note that the salt-bridge interactions depicted in Liu (3MD2) are>3.7 Å. Green transparent boxes within the rectangles represent the relative amount of shared interfacial surface area (Table 2).