The Matrix Protein VP40 from Ebola Virus Octamerizes into Pore-like Structures with Specific RNA Binding Properties

Abstract

The Ebola virus membrane-associated matrix protein VP40 is thought to be crucial for assembly and budding of virus particles. Here we present the crystal structure of a disk-shaped octameric form of VP40 formed by four antiparallel homodimers of the N-terminal domain. The octamer binds an RNA triribonucleotide containing the sequence 5'-U-G-A-3' through its inner pore surface, and its oligomerization and RNA binding properties are facilitated by two conformational changes when compared to monomeric VP40. The selective RNA interaction stabilizes the ring structure and confers in vitro SDS resistance to octameric VP40. SDS-resistant octameric VP40 is also found in Ebola virus-infected cells, which suggests that VP40 has an additional function in the life cycle of the virus besides promoting virus assembly and budding off the plasma membrane.

Crystal structure of the Borna disease virus matrix protein (BDV-M) reveals ssRNA binding properties

“…The exposed nature of ssRNA binding suggested by the present structure is quite different to that observed in octamers of the VP40 N-terminal domain (18), where the oligonucleotides are threaded through the axial octameric pore between adjacent dimeric molecules (Fig. S3).…”

“…Monomeric VP40 is composed of 2 structurally related domains of 200 (N-terminal) and 125 (Cterminal) residues (17), to which BDV-M exhibits rmsds of 1.8 Å (61 matched residues) and 2.1 Å (48 matched residues), respectively; the latter value is comparable with superposition of the VP40 N-and C-terminal domains themselves (1.8 Å for 56 matched residues). BDV-M and the VP40 N-terminal domain differ mainly in the lengths and orientation of loops and helices; interestingly, octameric structures of the VP40 N-terminal domain, found to bind RNA oligonucleotides (18), diverge from that of monomeric VP40 in the same regions (Fig. S1).…”

“…In contrast to these pyrimidine bases, neither the size of the pocket nor the hydrogen-bonding pattern is suited to the binding of the bulky purine bases adenine and guanine. Surprisingly, RNA binding occurs on a face of the monomer opposite to that corresponding to the trinucleotide binding site in VP40 octamers (18) (Fig. S1 and Fig.…”

“…Despite functional and structural homology with VP40, membrane binding modes appear to differ significantly between the 2 viruses. VP40 has been observed in multiple oligomeric forms; oligomerization occurs via the N-terminal domain to form monomeric, dimeric, hexameric, and octameric species (10,17,18,(30)(31)(32). In contrast, BDV-M has been observed in only 2 oligomeric states (15,16), namely tetramers and octamers.…”

“…Structures of protease-resistant M-protein fragments from 3 NSVs have been reported to date: VP40 from Ebola virus (17,18), M from VSV (19), and M1 from influenza virus (20,21). These M-proteins exhibit neither sequence nor structural homology to one other (10).…”