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      Structural basis for nuclear import of hepatitis B virus (HBV) nucleocapsid core

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          Abstract

          Nuclear import of the hepatitis B virus (HBV) nucleocapsid is essential for replication that occurs in the nucleus. The ~360-angstrom HBV capsid translocates to the nuclear pore complex (NPC) as an intact particle, hijacking human importins in a reaction stimulated by host kinases. This paper describes the mechanisms of HBV capsid recognition by importins. We found that importin α1 binds a nuclear localization signal (NLS) at the far end of the HBV coat protein Cp183 carboxyl-terminal domain (CTD). This NLS is exposed to the capsid surface through a pore at the icosahedral quasi-sixfold vertex. Phosphorylation at serine-155, serine-162, and serine-170 promotes CTD compaction but does not affect the affinity for importin α1. The binding of 30 importin α1/β1 augments HBV capsid diameter to ~620 angstroms, close to the maximum size trafficable through the NPC. We propose that phosphorylation favors CTD externalization and prompts its compaction at the capsid surface, exposing the NLS to importins.

          Abstract

          Hepatitis B virus capsid recognition by human importins was deciphered by combining structural and computational methods.

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          UCSF Chimera--a visualization system for exploratory research and analysis.

          The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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            CTFFIND4: Fast and accurate defocus estimation from electron micrographs.

            CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.
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              UCSF ChimeraX: Meeting modern challenges in visualization and analysis

              UCSF ChimeraX is next‐generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting‐edge experimental methods, while providing advanced options for high‐quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax / for Windows, Mac, and Linux.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: Visualization
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: Validation
                Role: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SoftwareRole: Validation
                Role: InvestigationRole: Resources
                Role: Formal analysisRole: InvestigationRole: Visualization
                Role: Formal analysisRole: InvestigationRole: Visualization
                Role: Formal analysisRole: InvestigationRole: Writing - original draft
                Role: Formal analysisRole: Investigation
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: ResourcesRole: SupervisionRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Journal
                Sci Adv
                Sci Adv
                sciadv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                12 January 2024
                10 January 2024
                : 10
                : 2
                : eadi7606
                Affiliations
                [ 1 ]Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.
                [ 2 ]Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA.
                [ 3 ]Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, IN 47405, USA.
                [ 4 ]Department of Chemistry, Indiana University, Bloomington, Indiana, IN 47405, USA.
                [ 5 ]Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
                Author notes
                [* ]Corresponding author. Email: gcingola@ 123456uab.edu (G.C.); jhadden@ 123456udel.edu (J.A.H.-P.)
                Author information
                https://orcid.org/0000-0003-4846-3541
                https://orcid.org/0000-0003-4240-9923
                https://orcid.org/0000-0001-7932-0071
                https://orcid.org/0000-0002-1820-9588
                https://orcid.org/0009-0007-4913-4797
                https://orcid.org/0009-0006-9415-9873
                https://orcid.org/0009-0000-3134-6782
                https://orcid.org/0000-0002-8766-789X
                https://orcid.org/0000-0001-9945-6267
                https://orcid.org/0000-0003-4685-8291
                https://orcid.org/0000-0002-9206-9640
                Article
                adi7606
                10.1126/sciadv.adi7606
                10780889
                38198557
                44883c3a-b04a-42ab-9ff7-98cb49820a77
                Copyright © 2024 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                History
                : 17 May 2023
                : 08 December 2023
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: MCB-2238190
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01 GM100888
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R35 GM140733
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: S10 OD017987
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: S10 OD023479
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: S10 OD030457
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: AI144022
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: U24 GM129539
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: U24 GM129541
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: P30 CA56036
                Funded by: FundRef http://dx.doi.org/10.13039/100000054, National Cancer Institute;
                Award ID: 75N91019D00024
                Funded by: FundRef http://dx.doi.org/10.13039/100000893, Simons Foundation;
                Award ID: SF349247
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: R01GM116961
                Funded by: FundRef http://dx.doi.org/10.13039/100019206, Delta Electronics;
                Award ID: BIO-230104
                Funded by: FundRef http://dx.doi.org/10.13039/501100020414, Neurosciences Foundation;
                Award ID: 2138259
                Funded by: FundRef http://dx.doi.org/10.13039/501100020414, Neurosciences Foundation;
                Award ID: 2138286
                Funded by: FundRef http://dx.doi.org/10.13039/501100020414, Neurosciences Foundation;
                Award ID: 2138307
                Funded by: FundRef http://dx.doi.org/10.13039/501100020414, Neurosciences Foundation;
                Award ID: 2137603
                Funded by: FundRef http://dx.doi.org/10.13039/501100020414, Neurosciences Foundation;
                Award ID: 2138296
                Funded by: FundRef http://dx.doi.org/10.13039/501100020414, Neurosciences Foundation;
                Award ID: OAC-1919839
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: P20GM103446
                Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: S10OD028725
                Funded by: NY State Assembly;
                Categories
                Research Article
                Biomedicine and Life Sciences
                SciAdv r-articles
                Structural Biology
                Virology
                Structural Biology
                Custom metadata
                Jeanelle Ebreo

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