Structure of a rabies virus polymerase complex from electron cryo-microscopy

Abstract

Non-segmented negative-stranded (NNS) RNA viruses, among them the virus that causes rabies (RABV), include many deadly human pathogens. The large polymerase (L) proteins of NNS-RNA viruses carry all the enzymatic functions required for viral mRNA transcription and replication: RNA polymerization, mRNA capping, cap methylation. We describe here a complete structure of RABV L bound with its phosphoprotein cofactor (P), determined by electron cryo-microscopy at 3.3 Å resolution. The complex closely resembles vesicular stomatitis virus (VSV) L-P, the one other known full-length NNS-RNA L protein structure, with key local differences (e.g., in L-P interactions). Like the VSV L-P structure, the RABV complex analyzed here represents a pre-initiation conformation. Comparison with the likely elongation state, seen in two partial structures of pneumovirus L-P complexes, suggests differences between priming/initiation and elongation complexes. Analysis of internal cavities within RABV L suggests distinct template and product entry and exit pathways during transcription and replication.

Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor

“…The interaction of rabies virus (RABV) P with RABV L is similar the VSV P-L interaction described here ( Figure S4C), with contacts that anchor the CD, MT, and CTD and stabilize a closed conformation of L (Horwitz et al, 2019). The P L sequences for the two viruses have diverged substantially, however, and the specific molecular interactions differ.…”

Therapeutic Targeting of Measles Virus Polymerase with ERDRP-0519 Suppresses All RNA Synthesis Activity

“…We favor the mononegavirus RdRP complex as a premier druggable target, based on its diverse enzymatic activities, its unique catalytic activity that lacks a cellular equivalent, and its critical importance for both viral replication and the expression of non-structural immunomodulatory viral proteins that counteract the host innate antiviral response (45). Groundbreaking progress in the structural understanding of the organization of mononegavirus polymerase complexes (29)(30)(31)(32) has established a foundation to define distinct druggable sites in the L polymerase.…”

“…This delayed polymerase arrest demonstrates that these compounds do not directly block phosphodiester bond formation. Structural evidence (29)(30)(31)(32)46) and functional characterization (27,34) rather indicates pharmacological interference with conformational changes of the polymerase as the enzyme transitions from initiation to RNA elongation mode.…”

“…Despite this high clinical promise, the molecular mechanism of polymerase inhibition by ERDRP-0519 and its physical target docking pose remained unknown, creating a knowledge gap hampering development of the inhibitor class against other mononegavirus targets. Several structural reconstructions of mononegavirus polymerase have been reported recently Cox et al 6 that provided essential insight into the organization of rhabdovirus (vesicular stomatitis virus and rabies virus (29,30)), pneumovirus (RSV (31)), and paramyxovirus (parainfluenzavirus 5 (PIV-5) (32)) polymerase complexes. This information established a framework for structural and mechanistic appreciation of polymerase inhibition by ERDRP-0519.…”

Insight into the multifunctional RNA synthesis machine of rabies virus

“…In humans, rabies is preventable by vaccination prior to or immediately after exposure, but there are no specific antiviral drugs available that target the virus directly (1). In PNAS, Horwitz et al (2) present a high-resolution electron cryomicroscopy structure of the RNA synthesis machine of RABV, providing valuable mechanistic insight into its activities and opening up the way toward developing antiviral approaches for this fatal virus.…”