6XW7
Crystal structure of murine norovirus P domain in complex with Nanobody NB-5829 and glycochenodeoxycholate (GCDCA)
Summary for 6XW7
| Entry DOI | 10.2210/pdb6xw7/pdb |
| Descriptor | Capsid protein, Nanobody NB-5829, 1,2-ETHANEDIOL, ... (6 entities in total) |
| Functional Keywords | mnv, neutralizing nanobody, vhh, norovirus, viral protein |
| Biological source | Murine norovirus 1 More |
| Total number of polymer chains | 8 |
| Total formula weight | 190846.79 |
| Authors | Kilic, T.,Sabin, C.,Hansman, G. (deposition date: 2020-01-23, release date: 2020-04-22, Last modification date: 2024-10-23) |
| Primary citation | Koromyslova, A.D.,Devant, J.M.,Kilic, T.,Sabin, C.D.,Malak, V.,Hansman, G.S. Nanobody-Mediated Neutralization Reveals an Achilles Heel for Norovirus. J.Virol., 94:-, 2020 Cited by PubMed Abstract: Human norovirus frequently causes outbreaks of acute gastroenteritis. Although discovered more than five decades ago, antiviral development has, until recently, been hampered by the lack of a reliable human norovirus cell culture system. Nevertheless, a lot of pathogenesis studies were accomplished using murine norovirus (MNV), which can be grown routinely in cell culture. In this study, we analyzed a sizeable library of nanobodies that were raised against the murine norovirus virion with the main purpose of developing nanobody-based inhibitors. We discovered two types of neutralizing nanobodies and analyzed the inhibition mechanisms using X-ray crystallography, cryo-electron microscopy (cryo-EM), and cell culture techniques. The first type bound on the top region of the protruding (P) domain. Interestingly, this nanobody binding region closely overlapped the MNV receptor-binding site and collectively shared numerous P domain-binding residues. In addition, we showed that these nanobodies competed with the soluble receptor, and this action blocked virion attachment to cultured cells. The second type bound at a dimeric interface on the lower side of the P dimer. We discovered that these nanobodies disrupted a structural change in the capsid associated with binding cofactors (i.e., metal cations/bile acid). Indeed, we found that capsids underwent major conformational changes following addition of Mg or Ca Ultimately, these nanobodies directly obstructed a structural modification reserved for a postreceptor attachment stage. Altogether, our new data show that nanobody-based inhibition could occur by blocking functional and structural capsid properties. This research discovered and analyzed two different types of MNV-neutralizing nanobodies. The top-binding nanobodies sterically inhibited the receptor-binding site, whereas the dimeric-binding nanobodies interfered with a structural modification associated with cofactor binding. Moreover, we found that the capsid contained a number of vulnerable regions that were essential for viral replication. In fact, the capsid appeared to be organized in a state of flux, which could be important for cofactor/receptor-binding functions. Blocking these capsid-binding events with nanobodies directly inhibited essential capsid functions. Moreover, a number of MNV-specific nanobody binding epitopes were comparable to human norovirus-specific nanobody inhibitors. Therefore, this additional structural and inhibition information could be further exploited in the development of human norovirus antivirals. PubMed: 32321816DOI: 10.1128/JVI.00660-20 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.15 Å) |
Structure validation
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