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      A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins

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          Abstract

          Dengue virus (DENV) infects ~400 million people annually. There is no licensed vaccine or therapeutic drug. Only a small fraction of the total DENV-specific antibodies in a naturally occurring dengue infection consists of highly neutralizing antibodies. Here we show that the DENV-specific human monoclonal antibody 5J7 is exceptionally potent, neutralizing 50% of virus at nanogram-range antibody concentration. The 9 Å resolution cryo-electron microscopy structure of the Fab 5J7–DENV complex shows that a single Fab molecule binds across three envelope proteins and engages three functionally important domains, each from a different envelope protein. These domains are critical for receptor binding and fusion to the endosomal membrane. The ability to bind to multiple domains allows the antibody to fully coat the virus surface with only 60 copies of Fab, that is, half the amount compared with other potent antibodies. Our study reveals a highly efficient and unusual mechanism of molecular recognition by an antibody.

          Abstract

          There is no licensed vaccine or therapeutic for dengue virus (DENV) infection. Here, the authors show that a highly potent human monoclonal antibody binds to DENV particles in an unusual and very effective way by interacting with three viral envelope proteins.

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          Most cited references46

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          Improved methods for building protein models in electron density maps and the location of errors in these models.

          Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.
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            Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.

            A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented. The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically correct. The molecular dynamics flexible fitting (MDFF) method is validated for available crystal structures of protein and RNA in different conformations; measures to assess and monitor the fitting process are introduced. The MDFF method is then used to obtain high-resolution structures of the E. coli ribosome in different functional states imaged by cryo-EM.
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              Structure of the dengue virus envelope protein after membrane fusion.

              Dengue virus enters a host cell when the viral envelope glycoprotein, E, binds to a receptor and responds by conformational rearrangement to the reduced pH of an endosome. The conformational change induces fusion of viral and host-cell membranes. A three-dimensional structure of the soluble E ectodomain (sE) in its trimeric, postfusion state reveals striking differences from the dimeric, prefusion form. The elongated trimer bears three 'fusion loops' at one end, to insert into the host-cell membrane. Their structure allows us to model directly how these fusion loops interact with a lipid bilayer. The protein folds back on itself, directing its carboxy terminus towards the fusion loops. We propose a fusion mechanism driven by essentially irreversible conformational changes in E and facilitated by fusion-loop insertion into the outer bilayer leaflet. Specific features of the folded-back structure suggest strategies for inhibiting flavivirus entry.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                20 February 2015
                : 6
                : 6341
                Affiliations
                [1 ]Program in Emerging Infectious Diseases, Duke–NUS Graduate Medical School , 8 College Road, Singapore 169857, Singapore
                [2 ]Centre for BioImaging Sciences, National University of Singapore , 14 Science Drive 4, Singapore 117557, Singapore
                [3 ]Department of Medicine, Vanderbilt University , 1161 21st Avenue South, D-3100 Medical Center North, Nashville, Tennessee 37232-2358, USA
                [4 ]The Vanderbilt Vaccine Center, Vanderbilt University,Vanderbilt University Medical Center , 11475 MRB IV—2213 Garland Avenue, Nashville, Tennessee 37232-0417, USA
                [5 ]Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , CB#7292, 9024 Burnett Womack, Chapel Hill, North Carolina 27599-7292, USA
                [6 ]Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University, Vanderbilt University Medical Center , 11475 MRB IV—2213 Garland Avenue, Nashville, Tennessee 37232-0417, USA
                Author notes
                [*]

                These authors contributed equally to this work

                Article
                ncomms7341
                10.1038/ncomms7341
                4346626
                25698059
                9ca8f315-1acd-46d1-b568-c8cd710bb036
                Copyright © 2015, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 15 April 2014
                : 21 January 2015
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