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| <!-- not used: Image:Workbench 3vi9 chain b.pdb.gz
| | #REDIRECT [[User:Fadel A. Samatey/FlgE I]] |
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| [[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br>
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| {{Clear}}<br>
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| <span style="border: 2px solid #a1a1a1; border-radius: 6px;padding:35px 50px 20px 30px;background: linear-gradient(#b0d0ff, #ffffff);"><span style="font-size:250%;">Scientific Reports</span>
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| <span style="padding: 0px 0px 0px 100px;color:#808080;font-size:120%;">an online, open access journal: [http://www.nature.com/srep nature.com/srep]</span></span>
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| {{Clear}}<br>
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| <span style="font-size:160%;line-height:130%;"><b>Structural insights into bacterial flagellar hook similarities and specifities.</b></span>
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| <br>
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| <span style="font-size:120%; line-height:160%;">Young-Ho '''Yoon''', Clive S. '''Barker''', Paula V. '''Bulieris''', Hideyuki '''[[User:Hideyuki_Matsunami|Matsunami]]''', and Fadel A. '''[[Fadel_A._Samatey_Group|Samatey]]'''.
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| <br>
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| ''Scientific Reports'' '''6''':35552, 2016: [http://www.nature.com/articles/srep35552 nature.com/articles/srep35552]. ([http://dx.doi.org/10.1038/srep35552 DOI: 10.1038/srep35552])
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| </span>
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| <br><br>
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| The interactive Molecular Tour below assumes that you are familiar with the journal article.
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| ==Molecular Tour==
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| <StructureSection size='450' side='right' caption=''
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| scene='User:Fadel_A._Samatey/Workbench/I3DC-2/Monomer_trace_n2c_rainbow/3'>
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| ==Monomer Structures==
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| ===''Campylobacter jejuni''===
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| The structure of the [[The Bacterial Flagellar Hook|flagellar hook]] monomer FlgE2 (gene Cj1729c) of ''Campylobacter jejuni'' (<scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Monomer_trace_n2c_rainbow/3'>restore initial scene</scene>) was determined to resolution 2.45 Å ([[5az4]]).
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| FlgE2 of ''C. jejuni'' (FlgE2-Cj; [http://www.uniprot.org/uniprot/Q0P7Q2 Q0P7Q2_CAMJE]) consists of 865 amino acids. The fragment crystallized<ref>PMID: 22139190</ref> was residues 91-828 (738 residues, 85% of full length). The crystallographic model has coordinates for residues 94-819 (726 residues, 84% of full length). The 79 kD fragment crystallized will be referred to as FlgE2-Cj79.
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| {{Template:ColorKey_N2CRainbow}}
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| <center>N->C Rainbow Color Scheme</center>
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| FlgE2-Cj is composed of <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Monomer_trace_n2c_rainbow/4'>five domains</scene> (D0-D4). D0 was not present in the fragment FlgE2-Cj79 in order to facilitate crystallization. D1-3 consist of discontinuous segments of the single protein chain, while D4 is one continuous segment. Here is a scene <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Monomer_trace_domain_colors/2'>colored by domain</scene>. The domains <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Monomer_cartoon_secstruct/2'>consist largely of antiparallel beta strands</scene>. D3 contains three alpha-helices while D4 contains one.
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| <center>{{Template:ColorKey_Helix}}, {{Template:ColorKey_Strand}}</center>
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| ===''Caulobacter crescentus''===
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| The structure of the [[The Bacterial Flagellar Hook|flagellar hook]] monomer FlgE (gene flgE) of ''Caulobacter cresentus'' <scene name='47/478822/Flge-cc/1'>was determined to resolution 1.84</scene> Å ([[5ay6]]).
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| {{Template:ColorKey_N2CRainbow}}
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| <center>N->C Rainbow Color Scheme</center>
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| FlgE of ''C. crecentus'' (FlgE-Cc; [http://www.uniprot.org/uniprot/P35806 P35806, FLGE_CAUCR], gene CC_0902) consists of 591 amino acids. The fragment crystallized was residues 165-470 (306 residues, 52% of full length). The crystallographic model has coordinates for residues 167-469 (303 residues, 51% of full length). The fragment crystallized is 32 kD, and will be referred to as FlgE-Cc32.
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| FlgE-Cc32 forms domains D2 and D3. D0 and D1 were removed to facilitate crystallization. D2 is formed by two discontinuous segments, while D3 is a single continuous segment inserted between the segments of D2. Here the model is <scene name='47/478822/Flge-cc/2'>colored by domains D2 and D3</scene>.
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| ==Comparison with ''Salmonella''==
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| FlgE (gene STM1177) of ''Salmonella enterica'' serotype Typhimurium (FlgE-St, [http://www.uniprot.org/uniprot/P0A1J1 P0A1J1_SALTY]) contains 403 amino acids, compared to the 865 in FlgE-Cj. However, the D1 and D2 domains are very similar in the two species (FlgE-St42: [[1wlg]]).
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| <center>
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| This animation takes ~2 minutes. Reload the page to cancel.
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| <jmol>
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| <jmolButton>
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| <script>background black;script /wiki/images/9/9a/Cj_St_FlgE_alignment_animation.spt;</script>
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| <text>Animate Structural Alignment</text>
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| </jmolButton>
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| </jmol>
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| </center>
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| FlgE-Cj contains the additional domains D3 and D4, making it a "hook with a hat".
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| A small adjustment in the angle between D1 and D2 in FlgE-Cj79 (a reduction of about 12<sup>o</sup>) enables <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/D1-d2-adjusted-alignment/1'>a very good structural alignment</scene> with FlgE-St42 (RMSD for 137 of 287 alpha carbons: 0.94 Å). The adjustment can also be <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Cj_d1d1_adj_morf/1'>visualized as a morph</scene>.
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| <center>
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| {{Template:Button_Toggle_Animation2}}
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| </center>
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| There is also close structural similarity between domains D1 and D2 comparing FlgE-Cc32 with FlgE-St42, and comparing Flg-Cj79 with Flg-Cc32 (Supplementary Fig. 3 in the journal article).
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| <!--==Crystal Contacts & Temperature==
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| IF REINSTATED, EVERY SCENE MUST BE RE-SAVED WITH 'RELOAD MOLECULE EVERY TIME' OPTION CHECKED.
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| The [[asymmetric unit]] contains <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Tetramer/1'>four chains</scene> (each chain shown a different color) but their contacts are a result of crystallization. In its biological function, the monomer of FlgE assembles into a hook filament composed of protofilaments (see below) with contacts unrelated to those in the crystal asymmetric unit.
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| When <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Tetramer/2'>colored by ''N to C Rainbow'',</scene> the D1 domains (<font color='red'><b>red</b></font> and <font color='blue'><b>blue</b></font>) protrude from the ends of the asymmetric unit.
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| The [[Temperature value|temperature]] (B-value; <scene name='User:Fadel_A._Samatey/Workbench/I3DC-2/Tetramer/3'>apply temperature colors</scene>) shows that the D1 domain has higher uncertainty (poorer fit to the electron density map) than do the D2-D4 domains.
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| {{Template:ColorKey_TemperatureFixed}}
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| <center>Absolute B-Factor Color Scheme</center>
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| The high temperature of D1 is despite some ***crystal contacts*** to D1 as well as D2-D4: crystal contact atoms within 4.0 Å of the asymmetric unit are shown as spacefilled atoms decorating the ribbon-asymmetric-unit.
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| -->
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| <!-- LATER?
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| ==Structure of Hook==
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| The flagellar hook of ''Salmonella'' consists of 132 monomer protein chains, assembled into 12 rings of 11 monomers, stacked to form 11 protofilaments<ref>PMID:15510139</ref><ref>PMID:15657146</ref><ref>PMID: 19913483</ref>. A putative model of the ''Campylobacter'' flagellar hook was constructed by homology with that of ''Salmonella''. Press the button below to see an interactive animation simulating assembly of 33 monomers into 25% of the putative hook.
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| <center>
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| This animation takes ~1.5 minutes. Reload the page to cancel.
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| <jmol>
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| <jmolButton>
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| <script>script /wiki/images/e/ee/Workshop_Cj_hook_assy.spt.gz;</script>
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| <text>Animate Hook Assembly</text>
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| </jmolButton>
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| </jmol>
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| </center>
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| In actuality, the hook is assembled by the flagellar basal body, not in a vacuum. Hook monomers are believed to be secreted through a central channel in the basal body prior to assembly, as shown in a movie available at [[Flagella, bacterial|Bacterial Flagella]].
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| -->
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| <hr>
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| </StructureSection>
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| ==Notes and References==
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| <references />
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