User:Fadel A. Samatey/FlgE II/Complete Flagellar Hook Structure

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.

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. 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 as in Fig. 2b-f, except that the L-stretch is yellow: Domain 4: Domain 3: Domain 2: Domain 1:  Domain 0 L-stretch:   Domain 0 Helices: 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 Channel All 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) and the C-terminal alpha helix (residues 812-851). 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 . Hydrophobic, Polar Although the inside surface of the channel is hydrophilic (polar), it contains . Anionic (-) / Cationic (+) 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 , for contrast in this scene: Here, the monomer is from neighboring monomers in the hook assembly. The contacting atoms are enlarged, and colored by domain. We can now see the following: Domain 0 Helices: Most neighbor contacts are from D0 helices. A few are from neighboring D0 L-stretches.  Domain 0 L-Stretch : Nearly all of the many neighbor contacts are from D1. Domain 1: 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. Domain 2: Most contacts are from the D2 neighbors on both sides. There are also some contacts from D3, and a handful from D1 and D4. Domain 3: Most neighbor contacts are from D2 and D4. There appear to be no D3 to D3 contacts. Domain 4: Most neighbor contacts are from D3, with a single carbon atom contacting from D2. Here the . C O N S 83 contacting atoms (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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