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[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br>
{{Clear}}<br>

<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>
<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>

{{Clear}}<br>
<span style="font-size:160%;line-height:130%;"><b>Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions.</b></span>
<br>
<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]]'''.
<br>
''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])
</span>
<br><br>
The interactive Molecular Tour below assumes that you are familiar with the journal article<ref name="s3">PMID: 27811912</ref>.

==Molecular Tour==
<StructureSection load='' size='430' side='right' caption='' scene='47/478824/Cj_hook_55_cao_v2/5'>
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.

===Domains===
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:

*<font color="#00b0b0">'''Domain 4:'''</font> <jmol>
 <jmolLink>
  <script>if (~d4);display visible, d4; ~d4=false; else; hide (not visible), d4; ~d4=true; endif;
  </script>
  <text>off/on</text>
 </jmolLink>
</jmol>

*<font color="#b06800">'''Domain 3:'''</font> <jmol>
 <jmolLink>
  <script>if (~d3);display visible, d3; ~d3=false; else; hide (not visible), d3; ~d3=true; endif;
  </script>
  <text>off/on</text>
 </jmolLink>
</jmol>

*<font color="#00b000">'''Domain 2:'''</font> <jmol>
 <jmolLink>
  <script>if (~d2);display visible, d2; ~d2=false; else; hide (not visible), d2; ~d2=true; endif;
  </script>
  <text>off/on</text>
 </jmolLink>
</jmol>

*<font color="red">'''Domain 1:'''</font> <jmol>
 <jmolLink>
  <script>if (~d1);display visible, d1; ~d1=false; else; hide (not visible), d1; ~d1=true; endif;
  </script>
  <text>off/on</text>
 </jmolLink>
</jmol>

*<span style="color:yellow;background:black;">'''&nbsp;Domain 0 L-stretch: '''</span>&nbsp;<jmol>
 <jmolLink>
  <script>if (~d0l);display visible,d0l; ~d0l=false; else; hide (not visible),d0l; ~d0l=true; endif;
  </script>
  <text>off/on</text>
 </jmolLink>
</jmol>

*<font color="#e000e0">'''Domain 0 Helices:'''</font> <jmol>
 <jmolLink>
  <script>if (~d0);display visible,d0; ~d0=false; else; hide (not visible),d0; ~d0=true; endif;
  </script>
  <text>off/on</text>
 </jmolLink>
</jmol>
The above switches also work on the <scene name='47/478824/Cj_hook_55_cao_v2/5'>initial scene</scene>.

===L-Stretch "Fingers"===
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.

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.

===Core and Channel===
All scenes in this subsection show only the D0 helices, with the D0 L-stretch, and D1-D4 hidden.

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><ref name="seqnum">Sequence numbers start with 1 at the second residue in the genomic sequence, since the initial Met is believed to be removed by N-terminal methionine aminopeptidase. The N-terminal genomic sequence (Uniprot FLGE-CAMJE Q0P7Q2) is MMRSLW, while the N-terminal sequence of the mature protein is believed to be MRSLW.</ref> and the <font color="red">'''C-terminal alpha helix (residues 812-851)'''</font><ref name="seqnum" />. 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:
<center>
<jmol>
<jmolButton>
<script>if (slabEnabled); slab off; else; slab 50; depth 0; slab on; endif;</script>
<text>Hide/Show Front Half</text>
</jmolButton>
</jmol>
</center>
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>.
<center><big>{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}</big></center>
Although the inside surface of the channel is hydrophilic (polar), it contains <scene name='47/478824/Hkcj_core/5'>no charged sidechains</scene>.
<center><big>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</big></center>
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.

===Contacts Between Monomers===
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<ref name="max">The monomer chain in the above scenes is chain "e". It is one of 21 chains in the 55-chain model that has the maximum number of contacting atoms (216) from other chains. It is also one of 28 chains that have the maximum number of atoms (51) from neighboring chains contacting the L-stretch. The L-stretch is also contacted by 31 atoms from other residues in the same chain (not shown).</ref> 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:

*<font color="#e000e0">'''Domain 0 Helices'''</font>: Most neighbor contacts are from D0 helices. A few are from neighboring D0 L-stretches.
*<span style="color:yellow;background:black;">'''&nbsp;Domain 0 L-Stretch&nbsp;'''</span>: Nearly all of the many neighbor contacts are from D1.
*<font color="red">'''Domain 1'''</font>: Most neighbor contacts are from D0 L-stretches, with a few also from D0 helices, D1 and D2.
*D0 and D1 have most of the contacts with neighbors. D2, D3 and D4 have fewer.
*<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.
*<font color="#b06800">'''Domain 3'''</font>: Most neighbor contacts are from D2 and D4. There appear to be no D3 to D3 contacts.
*<font color="#00b0b0">'''Domain 4'''</font>: Most neighbor contacts are from D3, with a single carbon atom contacting from D2.

Here the <scene name='47/478824/Hkcj_monomer_e10_v2/5'>216 contacting atoms are colored by element</scene><ref name="max" />.
<center><big>{{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_S}}</big></center>
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<ref name="seqnum" /> 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.
<center>--- The End ---</center>
</StructureSection>

==See Also==
* [[The Bacterial Flagellar Hook]]
* [[User:Fadel A. Samatey/FlgE I|X-ray structure of the hook monomers of ''Campylobacter jejuni'' and also of ''Caulobacter cresentus'']] (2016)
* [[User:Fadel A. Samatey/FlgE III/Intrinsically Disordered Flagellar Rod Stretch|FlgE III/Intrinsically Disordered Flagellar Rod Stretch]]
* [[Flagella, bacterial]]
==Notes and References==
<references />
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