Techniques and tactics used in determining the structure of the trimeric ebolavirus glycoprotein

Jeffrey E. Lee, Marnie L. Fusco, Dafna M. Abelson, Ann J. Hessell, Dennis R. Burton, Erica Ollmann Saphire

    Research output: Contribution to journalArticle

    22 Scopus citations

    Abstract

    The trimeric membrane-anchored ebolavirus envelope glycoprotein (GP) is responsible for viral attachment, fusion and entry. Knowledge of its structure is important both for understanding ebolavirus entry and for the development of medical interventions. Crystal structures of viral glycoproteins, especially those in their metastable prefusion oligomeric states, can be difficult to achieve given the challenges in production, purification, crystallization and diffraction that are inherent in the heavily glycosylated flexible nature of these types of proteins. The crystal structure of ebolavirus GP in its trimeric prefusion conformation in complex with a human antibody derived from a survivor of the 1995 Kikwit outbreak has now been determined [Lee et al. (2008), Nature (London), 454, 177-182]. Here, the techniques, tactics and strategies used to overcome a series of technical roadblocks in crystallization and phasing are described. Glycoproteins were produced in human embryonic kidney 293T cells, which allowed rapid screening of constructs and expression of protein in milligram quantities. Complexes of GP with an antibody fragment (Fab) promoted crystallization and a series of deglycosylation strategies, including sugar mutants, enzymatic deglycosylation, insect-cell expression and glycan anabolic pathway inhibitors, were attempted to improve the weakly diffracting glyco-protein crystals. The signal-to-noise ratio of the search model for molecular replacement was improved by determining the structure of the uncomplexed Fab. Phase combination with Fab model phases and a selenium anomalous signal, followed by NCS-averaged density modification, resulted in a clear interpretable electron-density map. Model building was assisted by the use of B-value-sharpened electron-density maps and the proper sequence register was confirmed by building alternate sequences using N-linked glycan sites as anchors and secondary-structural predictions.

    Original languageEnglish (US)
    Pages (from-to)1162-1180
    Number of pages19
    JournalActa Crystallographica Section D: Biological Crystallography
    Volume65
    Issue number11
    DOIs
    StatePublished - Dec 1 2009

    Keywords

    • Antibody complexes
    • Deglycosylation
    • Difficult structures
    • Glycoproteins
    • Human proteins
    • Model building
    • Structure determination
    • Tactics to improve diffraction
    • Techniques for phase determination
    • Viral proteins

    ASJC Scopus subject areas

    • Structural Biology

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