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

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.

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)^[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 Monomers

The , 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:

• 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 ^[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.