Cryoelectron Tomography of HIV-1 Envelope Spikes: Further Evidence for Tripod-Like Legs
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{"title"=>"Cryoelectron tomography of HIV-1 envelope spikes: Further evidence for tripod-like legs", "type"=>"journal", "authors"=>[{"first_name"=>"Ping", "last_name"=>"Zhu", "scopus_author_id"=>"56683874300"}, {"first_name"=>"Hanspeter", "last_name"=>"Winkler", "scopus_author_id"=>"7201676641"}, {"first_name"=>"Elena", "last_name"=>"Chertova", "scopus_author_id"=>"6602782383"}, {"first_name"=>"Kenneth A.", "last_name"=>"Taylor", "scopus_author_id"=>"35557662000"}, {"first_name"=>"Kenneth H.", "last_name"=>"Roux", "scopus_author_id"=>"7005744159"}], "year"=>2008, "source"=>"PLoS Pathogens", "identifiers"=>{"issn"=>"15537366", "pui"=>"352773709", "scopus"=>"2-s2.0-57149107577", "pmid"=>"19008954", "doi"=>"10.1371/journal.ppat.1000203", "isbn"=>"1553-7374 (Electronic)", "sgr"=>"57149107577"}, "id"=>"a3ced80a-9af2-3df2-9018-dcc3d24948c0", "abstract"=>"A detailed understanding of the morphology of the HIV-1 envelope (Env) spike is key to understanding viral pathogenesis and for informed vaccine design. We have previously presented a cryoelectron microscopic tomogram (cryoET) of the Env spikes on SIV virions. Several structural features were noted in the gp120 head and gp41 stalk regions. Perhaps most notable was the presence of three splayed legs projecting obliquely from the base of the spike head toward the viral membrane. Subsequently, a second 3D image of SIV spikes, also obtained by cryoET, was published by another group which featured a compact vertical stalk. We now report the cryoET analysis of HIV-1 virion-associated Env spikes using enhanced analytical cryoET procedures. More than 2,000 Env spike volumes were initially selected, aligned, and sorted into structural classes using algorithms that compensate for the \"missing wedge'' and do not impose any symmetry. The results show varying morphologies between structural classes: some classes showed trimers in the head domains; nearly all showed two or three legs, though unambiguous three-fold symmetry was not observed either in the heads or the legs. Subsequently, clearer evidence of trimeric head domains and three splayed legs emerged when head and leg volumes were independently aligned and classified. These data show that HIV-1, like SIV, also displays the tripod-like leg configuration, and, unexpectedly, shows considerable gp41 leg flexibility/heteromorphology. The tripod-like model for gp41 is consistent with, and helps explain, many of the unique biophysical and immunological features of this region.", "link"=>"http://www.mendeley.com/research/cryoelectron-tomography-hiv1-envelope-spikes-further-evidence-tripodlike-legs", "reader_count"=>68, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>8, "Researcher"=>15, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>6, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>11, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>8, "Researcher"=>15, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>6, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>11, "Professor"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Biochemistry, Genetics and Molecular Biology"=>4, "Materials Science"=>3, "Agricultural and Biological Sciences"=>38, "Medicine and Dentistry"=>10, "Chemistry"=>2, "Psychology"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>4, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Materials Science"=>{"Materials Science"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>10}, "Chemistry"=>{"Chemistry"=>2}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>38}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}}, "reader_count_by_country"=>{"United States"=>3, "China"=>1, "Portugal"=>1, "Switzerland"=>1, "Germany"=>1, "Spain"=>1, "Russia"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/915632"], "description"=>"<p>The selected (whole) HIV-1 spikes were aligned and sorted into eight classes. For each class, the tilt axis direction of each spike was calculated with respect to the spike coordinate frame and mapped onto the surface of a unit sphere (red “+” symbols), which was then converted to a two-dimensional representation with a sinusoidal projection. Latitude 90 degrees (vertical coordinate), for instance, corresponds to a tilt axis direction along the spike axis pointing to the spike head, −90 degrees to the spike base. The sinusoidal projection preserves the area, so that the density of the plotted points is the same as on the spherical surface. Numbers in the upper right corner of each panel correspond to the class numbers illustrated in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000203#ppat-1000203-g003\" target=\"_blank\">Figure 3A</a>.</p>", "links"=>[], "tags"=>["hiv-1", "env"], "article_id"=>586089, "categories"=>["Virology"], "users"=>["Ping Zhu", "Hanspeter Winkler", "Elena Chertova", "Kenneth A. Taylor", "Kenneth H. Roux"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000203.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Spatial_distribution_of_the_HIV_1_Env_spikes_/586089", "title"=>"Spatial distribution of the HIV-1 Env spikes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:34:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/915776"], "description"=>"<p>Red spheres and green lines represent gp120 and gp41 subunits, respectively. (A) Possible modes of flexibility within any given Env spike (blue arrows). Cylindrical masks (blue) encompass the entire spike (B), the gp120 head region (C), or the gp41 leg region (D). Black arrows indicate translocation, rotation, and tilting applied during alignment.</p>", "links"=>[], "tags"=>["alignment", "classification", "schemes", "applied", "spike"], "article_id"=>586228, "categories"=>["Virology"], "users"=>["Ping Zhu", "Hanspeter Winkler", "Elena Chertova", "Kenneth A. Taylor", "Kenneth H. Roux"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000203.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_alignment_and_classification_schemes_applied_to_selected_spike_volumes_/586228", "title"=>"Schematic representation of the alignment and classification schemes applied to selected spike volumes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:35:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/915846"], "description"=>"<p>The various alignment and classification combinations are indicated (A–E) and refer back to the mask depictions in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000203#ppat-1000203-g002\" target=\"_blank\">Figure 2</a>. Eight classes were produced for each combination (1–8) and the numbers of individual spikes volumes in each class is indicated below the panels. For each exercise, ∼800 spikes were automatically discarded as not fitting any of the eight classes. The boxed insert depicts the approximate locations of the sections shown (H = transverse section through the head, L = transverse section through the legs, S = longitudinal section showing side view of the spike (above) and viral membrane (below)). Bar = 20 nm.</p>", "links"=>[], "tags"=>["transverse", "longitudinal", "sections", "aligned", "classified", "hiv-1", "env"], "article_id"=>586296, "categories"=>["Virology"], "users"=>["Ping Zhu", "Hanspeter Winkler", "Elena Chertova", "Kenneth A. Taylor", "Kenneth H. Roux"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000203.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representative_digital_transverse_and_longitudinal_sections_of_the_aligned_and_classified_HIV_1_Env_spikes_/586296", "title"=>"Representative digital transverse and longitudinal sections of the aligned and classified HIV-1 Env spikes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:35:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/915989"], "description"=>"<p>Alignment and classification combinations as presented in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000203#ppat-1000203-g002\" target=\"_blank\">Figure 2</a> and described in the text. The left (A,C,E) and right (B,D,F) panel pairs show the averaged spikes before (left) and after (right) symmetrization. Within each pair are side (left) and top (right) views. Panels (G) (unsymmetrized) and (H) (symmetrized) represent idealized chimeric models composed to the head regions of (C) and (D) grafted onto the legs of (E) and (F), respectively. (I) and (J) represent transverse digital sections through the head (a), waist (b), and membrane-proximal leg region (c) as indicated in (G) and (H).</p>", "links"=>[], "tags"=>["rendered", "models", "averaged"], "article_id"=>586447, "categories"=>["Virology"], "users"=>["Ping Zhu", "Hanspeter Winkler", "Elena Chertova", "Kenneth A. Taylor", "Kenneth H. Roux"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000203.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Surface_rendered_models_of_averaged_selected_classes_/586447", "title"=>"Surface rendered models of averaged selected classes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 07:36:36"}

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Relative Metric

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