Structure of the Vesicular Stomatitis Virus Nucleoprotein-RNA Complex

Abstract

Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.

Predictive and comparative analysis of Ebolavirus proteins

“…54 The N-terminal domain is likely shared among Mononegavirales. Known 3D structures of NP from several virus families [77][78][79][80][81] in this order possess the same topology ( Fig. 3A-D).…”

Crimean–Congo hemorrhagic fever virus nucleoprotein reveals endonuclease activity in bunyaviruses

“…S10), we found that the region of CCHFV equivalent to the RNA-binding LASV NP α6 helix is probably located at residues L181-S194, residues which are missing from our final structure due to their intrinsic structural flexibility. Currently, several structures of (−)ssRNA virus nucleoproteins have been reported, including rabies virus (13), VSV (14), and BDV (15). These three NP structures demonstrate that RNA binds nonspecifically in a deep positively charged groove.…”

“…To our knowledge, the only NP structure reported to date in the Bunyaviridae family is the Rift Valley fever virus nucleoprotein (9,10), which shows weak binding affinity with RNA and displays a conformational change before oligomerization into a ribonucleoprotein (RNP) complex (9). Previous structures of NPs from other families, such as the influenza virus (Orthomyxovidae) (11,12), rabies virus (Rhabdoviridae) (13), vesicular stomatitis virus (VSV) (Rhabdoviridae) (14), and borna disease virus (BDV) (Bornaviridae) (15) have shown how NPs assemble with RNA to form RNPs. Interestingly, recent studies by two research groups on the structure of the Lassa fever virus (LASV) (Arenaviridae) NP have added to our understanding of the functions of virally encoded NPs beyond their role in the packaging of viral genomic RNA (16)(17)(18).…”

Self-organization of the vesicular stomatitis virus nucleocapsid into a bullet shape

“…From this point on, two key unresolved questions are the mechanism of the ribbon function as a template for viral replication and transcription, and the mechanism of the ribbon-to-bullet transition during virion assembly. For the first question, progress has been achieved, thanks to the capacity of heterologously expressed rhabdoviral nucleoprotein to nonspecifically encapsidate not only long cellular RNAs but also short RNAs that noncovalently close up into N-RNA rings 1,2 . In the case of VSV, almost 80% of the rings contain 10 protomers of N 3 , suggesting that the decamer is their low energy form.…”

“…In the case of VSV, almost 80% of the rings contain 10 protomers of N 3 , suggesting that the decamer is their low energy form. The atomic structure of this artificially constrained arrangement was solved by X-ray crystallography 2 and provided insights into the structure of the nucleoprotein subunit, the nature of inter-subunit interactions, the mechanism of genome sequestering and the necessity of conformational rearrangements in the nucleoprotein required for access of the viral polymerase into the RNA-binding cleft 2,4 . For the second question, cryo-electron microscopy (cryoEM) analysis of the entire virion recently culminated in a 10 Å resolution threedimensional (3D) reconstruction of the skeleton trunk, where the viral matrix protein M, which role in the nucleocapsid condensation has been under debate since 30 years [5][6][7][8] , bridges consecutive turns of the N-RNA helix 1 .…”