Structure and mutagenesis reveal essential capsid protein interactions for KSHV replication

• Published in: Nature (London) Vol. 553; no. 7689; pp. 521 - 525
• Main Authors: Dai, Xinghong, Gong, Danyang, Lim, Hanyoung, Jih, Jonathan, Wu, Ting-Ting, Sun, Ren, Zhou, Z. Hong
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 25.01.2018; Nature Publishing Group
• Subjects: 101/28; 631/326/596/1553; 631/535/1258/1259; Amino acids; Antiviral agents; Atomic structure; Capsid - chemistry; Capsid - metabolism; Capsid - ultrastructure; Capsid protein; Capsid Proteins - chemistry; Capsid Proteins - genetics; Capsid Proteins - metabolism; Capsid Proteins - ultrastructure; Capsids; Chemical bonds; Crosslinking; Cryoelectron Microscopy; Deoxyribonucleic acid; Dimerization; Disulfide bonds; Disulfides - metabolism; DNA; Drug Design; Electron microscopy; Gene expression; Gene mapping; Genetic aspects; Genomes; Health aspects; Herpes viruses; Herpesvirus 8, Human - chemistry; Herpesvirus 8, Human - genetics; Herpesvirus 8, Human - growth & development; Herpesvirus 8, Human - ultrastructure; Human herpesvirus 8; Humanities and Social Sciences; Hydrophobic and Hydrophilic Interactions; Hydrophobicity; Kaposi's sarcoma; letter; Microscopy; Models, Molecular; Molecular interactions; Molecular structure; multidisciplinary; Mutagenesis; Mutant Proteins - chemistry; Mutant Proteins - genetics; Mutant Proteins - metabolism; Mutant Proteins - ultrastructure; Mutation; Polypeptides; Protein Binding; Protein Domains; Protein interaction; Protein Multimerization; Protein Stability; Protein-protein interactions; Proteins; Replication; Sarcoma; Science; Single-cell protein; Virus Replication - genetics
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature25438

Cryo-electron microscopy reveals the structure of the Kaposi’s sarcoma-associated herpesvirus capsid, and experiments with polypeptides that mimic the smallest capsid protein demonstrate the potential for structure-derived insights to help to develop antiviral agents. KSHV structure gives clues to stop viral replication Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS. KSHV is an enormous virus with nearly 3,000 proteins, which has made determining its structure challenging. Hong Zhou and colleagues used cryo-electron microscopy to solve the structure of KSHV's capsid to 4.2 Å resolution. Their atomic model, corroborated by mutagenesis analysis, reveals molecular interactions that are important for stabilizing the capsid. The authors show experimentally that these interactions can be exploited to inhibit virus replication. Kaposi’s sarcoma-associated herpesvirus (KSHV) causes Kaposi’s sarcoma 1 , 2 , a cancer that commonly affects patients with AIDS 3 and which is endemic in sub-Saharan Africa 4 . The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses 5 . Capsid assembly and genome packaging of herpesviruses are prone to interruption 6 , 7 , 8 , 9 and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids—comprising nearly 3,000 proteins and over 1,300 Å in diameter—present a formidable challenge to atomic structure determination 10 and functional mapping of molecular interactions. Here we report a 4.2 Å resolution structure of the KSHV capsid, determined by electron-counting cryo-electron microscopy, and its atomic model, which contains 46 unique conformers of the major capsid protein (MCP), the smallest capsid protein (SCP) and the triplex proteins Tri1 and Tri2. Our structure and mutagenesis results reveal a groove in the upper domain of the MCP that contains hydrophobic residues that interact with the SCP, which in turn crosslinks with neighbouring MCPs in the same hexon to stabilize the capsid. Multiple levels of MCP–MCP interaction—including six sets of stacked hairpins lining the hexon channel, disulfide bonds across channel and buttress domains in neighbouring MCPs, and an interaction network forged by the N-lasso domain and secured by the dimerization domain—define a robust capsid that is resistant to the pressure exerted by the enclosed genome. The triplexes, each composed of two Tri2 molecules and a Tri1 molecule, anchor to the capsid floor via a Tri1 N-anchor to plug holes in the MCP network and rivet the capsid floor. These essential roles of the MCP N-lasso and Tri1 N-anchor are verified by serial-truncation mutageneses. Our proof-of-concept demonstration of the use of polypeptides that mimic the smallest capsid protein to inhibit KSHV lytic replication highlights the potential for exploiting the interaction hotspots revealed in our atomic structure to develop antiviral agents.