A supramolecular assembly mediates lentiviral DNA integration

Abstract

Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo-electron microscopy, we now visualize the functional maedi-visna lentivirus intasome at 4.9 Å resolution. The intasome comprises a homo-hexadecamer of IN with a tetramer-of-tetramers architecture featuring eight structurally distinct types of IN protomers supporting two catalytically competent subunits. The conserved intasomal core, previously observed in simpler retroviral systems, is formed between two IN tetramers, with a pair of C-terminal domains from flanking tetramers completing the synaptic interface. Our results explain how HIV-1 IN, which self-associates into higher order multimers, can form a functional intasome, reconcile the bulk of early HIV-1 IN biochemical and structural data, and provide a lentiviral platform for design of HIV-1 IN inhibitors.

Retroviral intasomes arising

“…All of the CCD-CTD linkers in both structures assume nearly straight α-helical configurations, in agreement with crystallographic studies [7,27,28]. The CTD-CTD dimerization interface originally discovered via nuclear magnetic resonance spectroscopy is another previously underappreciated HIV-1 IN structure that is observed in the higher-order lentiviral intasome structures, but absent in the tetrameric Sso7d-IN intasome [7,21,33,34]. The remarkable conservation of the quaternary features in face of limited primary structure conservation between HIV-1 and MVV INs, which share less than 30% amino acid sequence identity [16], strongly argues for the relevance of the higher-order lentiviral assemblies.…”

“…Overall, the dodecameric HIV-1 Sso7d-IN and the hexadecameric MVV intasomes are remarkably similar, although the former is missing an IN dimer from each flank. All of the CCD-CTD linkers in both structures assume nearly straight α-helical configurations, in agreement with crystallographic studies [7,27,28]. The CTD-CTD dimerization interface originally discovered via nuclear magnetic resonance spectroscopy is another previously underappreciated HIV-1 IN structure that is observed in the higher-order lentiviral intasome structures, but absent in the tetrameric Sso7d-IN intasome [7,21,33,34].…”

“…Additional structures, which visualized the remaining PFV complexes along the integration pathway, were similarly reported over the ensuing 2 years (Figure 1) [2,5,6]. Today, the PFV intasome can be considered a minimalist assembly with the lowest order IN-to-viral DNA stoichiometry among retroviral intasomes characterized thus far [7]. Accordingly, we will overview its salient features before discussing the more complex assemblies that were elucidated only very recently.…”

“…However, recent intasome structures from four orthoretroviruses revealed both striking complexity and diversity. Reported from February 2016 to January 2017, the new structures elucidated intasomes from the β-retrovirus mouse mammary tumor virus (MMTV) [19], α-retrovirus Rous sarcoma virus (RSV) [20], lentivirus maedi-visna virus (MVV) [7], and lentivirus human immunodeficiency virus 1 (HIV-1) [21]. As three of the studies utilized single particle cryo-electron microscopy [7,19,21], much of the work benefited from the ongoing revolution in this structural biology platform (reviewed in [22]).…”

“…However, the required fully extended conformation is incompatible with IN crystallography studies that observed this region in a compact α-helical configuration [27,28]. Moreover, the CCD-CTD linker is predicted to be α-helical across divergent members of the lentiviral genus [7]. …”