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Samatey/4

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[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br>
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#REDIRECT [[User:Fadel_A._Samatey/FlgE_II/Complete_Flagellar_Hook_Structure]]
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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(#a0e0e0, #ffffff);white-space: nowrap;"><span style="font-size:200%;">Nature Communications</span>
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<span style="padding: 0px 0px 0px 50px;color:#808080;font-size:120%;">an online-only, open access journal: [http://www.nature.com/ncomms nature.com/ncomms]</span></span>
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{{Clear}}<br>
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<span style="font-size:160%;line-height:130%;"><b>Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions.</b></span>
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<br>
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<span style="font-size:120%; line-height:160%;">Hideyuki '''[[User:Hideyuki_Matsunami|Matsunami]]''', Clive S. '''Barker''', Young-Ho '''Yoon''', Matthias '''Wolf''', and Fadel A. '''[[Fadel_A._Samatey_Group|Samatey]]'''.
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<br>
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''Nature Communications'' '''7''':13425, 2016: [http://www.nature.com/articles/ncomms13425 nature.com/articles/ncomms13425]. ([http://dx.doi.org/10.1038/ncomms13425 DOI: 10.1038/ncomms13425])
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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<ref name="s3">(Waiting for PubMed)</ref>.
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==Molecular Tour==
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<StructureSection load='' size='430' side='right' caption='' scene='47/478824/Cj_hook_55_cao_v2/5'>
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The structure of the flagellar hook FlgE of ''Campylobacter jejuni'' strain 81116 (FlgE-Cj; [https://www.ncbi.nlm.nih.gov/protein/WP_012006803.1 NCBI WP_012006803]) was determined by cryo-electron microscopy to a resolution of 3.5 &Aring;. Initially we show a model containing 55 monomers of FlgE (<scene name='47/478824/Cj_hook_55_cao_v2/5'>restore initial scene</scene>). This model contains 349,965 non-hydrogen atoms. To make this model manageable, we are showing only the 48,805 alpha carbon atoms<ref>Alpha carbons are spacefilled to a radius of 3.5 &Aring; to make domains look solid. The van der Waals radius of carbon is 1.7 &Aring;.</ref>. Each of the 55 chains is given a distinct color.
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===Domains===
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FlgE-Cj has 5 domains, D0 through D4. D0 is made up of two helices, and an "L-stretch". Here <scene name='47/478824/Cj_hook_55_cao_v2/4'>the hook model is colored by domains</scene> as in Fig. 2b-f, except that the L-stretch is yellow:
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*<font color="#00b0b0">'''Domain 4:'''</font> <jmol>
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<jmolLink>
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<script>if (~d4);display visible, d4; ~d4=false; else; hide (not visible), d4; ~d4=true; endif;
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</script>
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<text>off/on</text>
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</jmolLink>
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</jmol>
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*<font color="#b06800">'''Domain 3:'''</font> <jmol>
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<jmolLink>
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<script>if (~d3);display visible, d3; ~d3=false; else; hide (not visible), d3; ~d3=true; endif;
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</script>
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<text>off/on</text>
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</jmolLink>
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</jmol>
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*<font color="#00b000">'''Domain 2:'''</font> <jmol>
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<jmolLink>
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<script>if (~d2);display visible, d2; ~d2=false; else; hide (not visible), d2; ~d2=true; endif;
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</script>
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<text>off/on</text>
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</jmolLink>
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</jmol>
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*<font color="red">'''Domain 1:'''</font> <jmol>
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<jmolLink>
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<script>if (~d1);display visible, d1; ~d1=false; else; hide (not visible), d1; ~d1=true; endif;
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</script>
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<text>off/on</text>
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</jmolLink>
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</jmol>
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*<span style="color:yellow;background:black;">'''&nbsp;Domain 0 L-stretch: '''</span>&nbsp;<jmol>
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<jmolLink>
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<script>if (~d0l);display visible,d0l; ~d0l=false; else; hide (not visible),d0l; ~d0l=true; endif;
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</script>
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<text>off/on</text>
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</jmolLink>
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</jmol>
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*<font color="#e000e0">'''Domain 0 Helices:'''</font> <jmol>
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<jmolLink>
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<script>if (~d0);display visible,d0; ~d0=false; else; hide (not visible),d0; ~d0=true; endif;
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</script>
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<text>off/on</text>
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</jmolLink>
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</jmol>
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The above switches also work on the <scene name='47/478824/Cj_hook_55_cao_v2/5'>initial scene</scene>.
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===L-Stretch "Fingers"===
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Use the above off/on switches to hide everything except D0. You will see "fingers" protruding from the D0 core of the hook. Each "finger" is an L-stretch portion of a D0 domain. Now show D1 and D0 (leaving D2-D4 hidden). You can see how the L-stretch fingers insert between copies of D1, interlinking D0 with D1.
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Here is <scene name='47/478824/Hkcj_monomer_chain_e10/9'>a single monomer protein chain of FlgE-Cj, colored by domain</scene> (see color key above). The L-stretch is in the D0 domain, and points "out to the side". Notice how it ends in a hook that will anchor itself between D1 domains.
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===Core and Channel===
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All scenes in this subsection show only the D0 helices, with the D0 L-stretch, and D1-D4 hidden.
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The <scene name='47/478824/Hkcj_core/2'>"core" of the hook</scene> is made up of the <font color="blue">'''N-terminal alpha helix (residues 1-31)'''</font> and the <font color="red">'''C-terminal alpha helix (residues 812-851)'''</font>. The inner surface of the channel is lined with the C-terminal helices, while the N-terminal helices form the outer layer of the core. This may be appreciated more clearly with <scene name='47/478824/Hkcj_core/3'>solid atoms (spacefilling, van der Waals radii)</scene>. To see the inside of the channel:
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<center>
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<jmol>
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<jmolButton>
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<script>if (slabEnabled); slab off; else; slab 50; depth 0; slab on; endif;</script>
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<text>Hide/Show Front Half</text>
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</jmolButton>
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</jmol>
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</center>
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The <scene name='47/478824/Hkcj_core/4'>inside of the channel is entirely hydrophilic</scene><ref>Polar residues are Arg, Asn, Asp, Gln, Glu, His, Lys, Ser, Thr, Tyr. There are no Tyr or Trp lining the channel.</ref>.
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<center><big>{{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}</big></center>
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Although the inside surface of the channel is hydrophilic (polar), it contains <scene name='47/478824/Hkcj_core/5'>no charged sidechains</scene>.
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<center><big>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</big></center>
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There is one salt bridge visible in the channel (Arg827:Asp840). Not only are the charges neutralized by the salt bridge, but careful examination shows that neither charge is on the inner surface of the channel.
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===Contacts Between Monomers===
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The <scene name='47/478824/Hkcj_monomer_e10_v2/3'>monomer domain colors are now lighter</scene>, for contrast in this scene: Here, the monomer is <scene name='47/478824/Hkcj_monomer_e10_v2/4'>decorated with all contacting atoms</scene> from neighboring monomers in the hook assembly. The contacting atoms<ref name="contacting">"Contacting" is defined as likely hydrogen bonds, plus likely apolar interactions. Likely hydrogen bonds: oxygens or nitrogens within 3.5 &Aring; of oxygens or nitrogens in a neighboring monomer. Apolar interactions: carbons or sulfurs within 4.0 &Aring; of carbons or sulfurs in a neighboring monomer.</ref> are enlarged<ref>Contacting atoms are rendered at radius 3.1 &Aring;. For comparison, the van der Waals radius of carbon is 1.7 &Aring;.: A. Bondi, ''J. Phys. Chem.'' '''68''':441 (1964).</ref>, and colored by domain. We can now see the following:
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*<font color="#e000e0">'''Domain 0 Helices'''</font>: Most neighbor contacts are from D0 helices. A few are from neighboring D0 L-stretches.
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*<span style="color:yellow;background:black;">'''&nbsp;Domain 0 L-Stretch&nbsp;'''</span>: Nearly all of the many neighbor contacts are from D1.
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*<font color="red">'''Domain 1'''</font>: Most neighbor contacts are from D0 L-stretches, with a few also from D0 helices, D1 and D2.
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*D0 and D1 have most of the contacts with neighbors. D2, D3 and D4 have fewer.
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*<font color="#00b000">'''Domain 2'''</font>: Most contacts are from the D2 neighbors on both sides. There are also some contacts from D3, and a handful from D1 and D4.
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*<font color="#b06800">'''Domain 3'''</font>: Most neighbor contacts are from D2 and D4. There appear to be no D3 to D3 contacts.
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*<font color="#00b0b0">'''Domain 4'''</font>: Most neighbor contacts are from D3, with a single carbon atom contacting from D2.
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Here the <scene name='47/478824/Hkcj_monomer_e10_v2/5'>216 contacting atoms are colored by element</scene>.
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<center><big>{{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_S}}</big></center>
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83 contacting atoms<ref name="contacting" /> (38%) are polar (oxygen, nitrogen), while 133 (62%) are apolar (132 carbon, 1 sulfur). The polar interactions include 20 neighbor atoms engaged in [[salt bridges]] (D0 helices:4, D0 L-stretch:3, D1:8, D2:2, D3:0, D4:3), and two [[cation-pi interactions]] (R58 in the tip of the L-stretch:F133 in D1). Thus 75% of the salt bridges and both cation-pi interactions contact D0 or D1, while only 25% of the salt bridges contact D2, D3 or D4. 109 (82%) of the apolar contacting atoms contact D0 or D1, while only 24 (11%) contact D2, D3 or D4.
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</StructureSection>
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==Notes and References==
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<references />
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Current revision

  1. REDIRECT User:Fadel_A._Samatey/FlgE_II/Complete_Flagellar_Hook_Structure

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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