User:Fadel A. Samatey/FlgE II/Complete Flagellar Hook Structure: Difference between revisions
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The interactive Molecular Tour below assumes that you are familiar with the journal article<ref name="s3"> | The interactive Molecular Tour below assumes that you are familiar with the journal article<ref name="s3">PMID: 27811912</ref>. | ||
==Molecular Tour== | ==Molecular Tour== | ||
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All scenes in this subsection show only the D0 helices, with the D0 L-stretch, and D1-D4 hidden. | 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> 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: | 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> | <center> | ||
<jmol> | <jmol> | ||
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===Contacts Between Monomers=== | ===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. 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 Å of oxygens or nitrogens in a neighboring monomer. Apolar interactions: carbons or sulfurs within 4.0 Å of carbons or sulfurs in a neighboring monomer.</ref> are enlarged<ref>Contacting atoms are rendered at radius 3.1 Å. For comparison, the van der Waals radius of carbon is 1.7 Å.: A. Bondi, ''J. Phys. Chem.'' '''68''':441 (1964).</ref>, and colored by domain. We can now see the following: | 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 Å of oxygens or nitrogens in a neighboring monomer. Apolar interactions: carbons or sulfurs within 4.0 Å of carbons or sulfurs in a neighboring monomer.</ref> are enlarged<ref>Contacting atoms are rendered at radius 3.1 Å. For comparison, the van der Waals radius of carbon is 1.7 Å.: 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. | *<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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*<font color="#00b0b0">'''Domain 4'''</font>: Most neighbor contacts are from D3, with a single carbon atom contacting from D2. | *<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>. | 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> | <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 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. | 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> | </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== | ==Notes and References== | ||
<references /> | <references /> | ||
Latest revision as of 01:20, 5 September 2021
Interactive 3D Complement in Proteopedia
Nature Communications an online-only, open access journal: nature.com/ncomms
Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions.
Hideyuki Matsunami, Clive S. Barker, Young-Ho Yoon, Matthias Wolf, and Fadel A. Samatey.
Nature Communications 7:13425, 2016: nature.com/articles/ncomms13425. (DOI: 10.1038/ncomms13425)
The interactive Molecular Tour below assumes that you are familiar with the journal article[1].
Molecular TourMolecular Tour
The structure of the flagellar hook FlgE of Campylobacter jejuni strain 81116 (FlgE-Cj; NCBI WP_012006803) was determined by cryo-electron microscopy to a resolution of 3.5 Å. Initially we show a model containing 55 monomers of FlgE (). This model contains 349,965 non-hydrogen atoms. To make this model manageable, we are showing only the 48,805 alpha carbon atoms[2]. Each of the 55 chains is given a distinct color. DomainsFlgE-Cj has 5 domains, D0 through D4. D0 is made up of two helices, and an "L-stretch". Here as in Fig. 2b-f, except that the L-stretch is yellow:
The above switches also work on the . 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 (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 ChannelAll scenes in this subsection show only the D0 helices, with the D0 L-stretch, and D1-D4 hidden. The is made up of the N-terminal alpha helix (residues 1-31)[3] and the C-terminal alpha helix (residues 812-851)[3]. 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 . To see the inside of the channel:
The [4]. Although the inside surface of the channel is hydrophilic (polar), it contains . 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 MonomersThe , for contrast in this scene: Here, the monomer is from neighboring monomers in the hook assembly[5] The contacting atoms[6] are enlarged[7], and colored by domain. We can now see the following:
Here the [5]. 83 contacting atoms[6] (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[3] 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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See AlsoSee Also
- The Bacterial Flagellar Hook
- X-ray structure of the hook monomers of Campylobacter jejuni and also of Caulobacter cresentus (2016)
- FlgE III/Intrinsically Disordered Flagellar Rod Stretch
- Flagella, bacterial
Notes and ReferencesNotes and References
- ↑ Matsunami H, Barker CS, Yoon YH, Wolf M, Samatey FA. Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Nat Commun. 2016 Nov 4;7:13425. doi: 10.1038/ncomms13425. PMID:27811912 doi:http://dx.doi.org/10.1038/ncomms13425
- ↑ Alpha carbons are spacefilled to a radius of 3.5 Å to make domains look solid. The van der Waals radius of carbon is 1.7 Å.
- ↑ 3.0 3.1 3.2 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.
- ↑ Polar residues are Arg, Asn, Asp, Gln, Glu, His, Lys, Ser, Thr, Tyr. There are no Tyr or Trp lining the channel.
- ↑ 5.0 5.1 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).
- ↑ 6.0 6.1 "Contacting" is defined as likely hydrogen bonds, plus likely apolar interactions. Likely hydrogen bonds: oxygens or nitrogens within 3.5 Å of oxygens or nitrogens in a neighboring monomer. Apolar interactions: carbons or sulfurs within 4.0 Å of carbons or sulfurs in a neighboring monomer.
- ↑ Contacting atoms are rendered at radius 3.1 Å. For comparison, the van der Waals radius of carbon is 1.7 Å.: A. Bondi, J. Phys. Chem. 68:441 (1964).