R1–R2 interdomain interactions. (A) R1–R2 contacts found in the R1–R7 structure determined in this work. The contacting residues at the interface are shown as sticks and labelled. Strands β2 and β3 of domain R1 form polar and hydrophobic interactions with the R2 residues located in the β2–β3 loop, strand β4 and in the interdomain linker. (B) View of the α-carbon trace of the recombinant R1–R7 (orange) with every five residues numbered. The structure of the equivalent region in the 3.5-Å structure of the complete vault (Tanaka et al, 2009) is superimposed (green). The residue numbers are written when structural correspondence was observed. (C) R1–R2 contacts found in the 3.5-Å structure.

Interdomain interactions at the interface between vault halves. (A) Ribbon diagram of the R1–R1 contacts at the half vault interface. The reference R1 domain (orange) contacts two consecutive R1 molecules (yellow) through the molecular two-fold axis. Interacting residues are shown in sticks and labelled. (B) Thirty-nine-fold averaged density of the vault particle at 8 Å resolution and inner view of the molecular surface of the central vault barrel. The electrostatic potential is represented in blue and red for the positive and negative charges, respectively. Nine R1–R7 protomers per half vault subunit are shown. The left side inset shows a close-up of the contacting residues at the interface between the two vault halves. The right side inset shows a close-up of the contacting interfaces between MVP protomers. Two consecutive R1–R7 molecules are shown. The amino acids involved in these lateral contacts are the same as that are shown in Figure 3. The electrostatic potential was calculated and rendered with PyMOL (DeLano, 2002), with colouring levels ranging from −66.7 to 66.7. (C) Schematic drawing, showing the mechanism of vault opening. At low pH, the acidic residues at the vault interface would become neutral, leaving a highly electropositive charge and inducing the disassembly of the vault particle by charge repulsion. At higher pH, the aspartate and glutamate residues, would present their acidic state establishing attractive electrostatic interactions between the two vault halves. The half vault moiety at the right side of the figure represents the flower-like structures described in Kedersha et al (1991).

The structure of the N-terminal fragment of MVP. (A) Ribbon representation of domain repeats R1–R7 showing the SSEs explicitly labelled. (B) Structural superimposition of the R1–R7 structures in the three different space groups P1 (orange), P2₁A (yellow) and P2₁B (light green). The Cα root mean square deviations are 0.42 and 0.45 Å for the superimposition of 220 residues, corresponding to the central R3–R6 domains, between the P1, P2₁A and P2₁B structures, respectively. (C) Structural superimposition of the R1–R7 fragments in the isolated R1–R7 structure (orange) and in the 3.5-Å structure of the complete vault (Tanaka et al, 2009) (green). Cα root mean square deviation is 0.9 Å for the superimposition of 150 Cα atoms, corresponding to the central R4–R6 domains.

R1–R7 packing contacts in the P1 crystal. Three R1–R7 fragments are represented in orange, the reference molecule and in yellow, the neighbour molecules in the crystal. The different boxes show the details of the interactions established between the different domains. Residues directly participating in hydrogen bonds or in hydrophobic contacts are shown as sticks and are explicitly labelled. The largest network of interactions involves R1 and R2 domains. R7 does not participate in lateral packing contacts.