User:Fadel A. Samatey/FlgE I

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Interactive 3D Complement in Proteopedia

Scientific Reports an online, open access journal: nature.com/srep

Structural insights into bacterial flagellar hook similarities and specifities.
Young-Ho Yoon, Clive S. Barker, Paula V. Bulieris, Hideyuki Matsunami, and Fadel A. Samatey.
Scientific Reports 6:35552, 2016: nature.com/articles/srep35552. (DOI: 10.1038/srep35552)

The interactive Molecular Tour below assumes that you are familiar with the journal article.

Molecular Tour

1 Monomer Structures
- 1.1 Campylobacter jejuni
- 1.2 Caulobacter crescentus
2 Comparison with Salmonella
3 Caulobacter Hook Model

Monomer Structures

Campylobacter jejuni

The structure of the flagellar hook monomer FlgE2 (gene Cj1729c) of Campylobacter jejuni () was determined to resolution 2.45 Å (5az4).

FlgE2 of C. jejuni (FlgE2-Cj; Q0P7Q2_CAMJE) consists of 865 amino acids. The fragment crystallized^[1] was residues 91-828 (738 residues, 85% of full length). The crystallographic model has coordinates for residues 94-819 (726 residues, 84% of full length). The 79 kD fragment crystallized will be referred to as FlgE2-Cj79.

N->C Rainbow Color Scheme

FlgE2-Cj is composed of (D0-D4). D0 was not present in the fragment FlgE2-Cj79 in order to facilitate crystallization. D1-3 consist of discontinuous segments of the single protein chain, while D4 is one continuous segment. Here is a scene . The domains . D3 contains three alpha-helices while D4 contains one.

Alpha Helices, Beta Strands

Caulobacter crescentus

The structure of the flagellar hook monomer FlgE (gene flgE) of Caulobacter cresentus Å (5ay6).

N->C Rainbow Color Scheme

FlgE of C. crecentus (FlgE-Cc; P35806, FLGE_CAUCR, gene CC_0902) consists of 591 amino acids. The fragment crystallized was residues 165-470 (306 residues, 52% of full length). The crystallographic model has coordinates for residues 167-469 (303 residues, 51% of full length). The fragment crystallized is 32 kD, and will be referred to as FlgE-Cc32.

FlgE-Cc32 forms domains D2 and D3. D0 and D1 were removed to facilitate crystallization. D2 is formed by two discontinuous segments, while D3 is a single continuous segment inserted between the segments of D2. Here the model is .

Comparison with Salmonella

FlgE (gene STM1177) of Salmonella enterica serotype Typhimurium^[2] (FlgE-St, P0A1J1_SALTY) contains 403 amino acids, compared to the 865 in FlgE-Cj. However, the D1 and D2 domains are very similar in the two species (FlgE-St42: 1wlg).

This animation takes ~2 minutes. Reload the page to cancel.

FlgE-Cj contains the additional domains D3 and D4, making it a "hook with a hat".

A small adjustment in the angle between D1 and D2 in FlgE-Cj79 (a reduction of about 12^o) enables with FlgE-St42 (RMSD for 137 of 287 alpha carbons: 0.94 Å). The adjustment can also be .

There is also close structural similarity between domains D1 and D2 comparing FlgE-Cc32 with FlgE-St42, and comparing FlgE2-Cj79 with FlgE-Cc32 (Supplementary Fig. 3 in the journal article).

Caulobacter Hook Model

A model of the hook of Caulobacter crecentus was made by manually docking the crystallographic structure of FlgE-Cc32 domains D2 and D3 into the 20 Å electron density map published in 1981^[3]. Here you can (alpha carbons only, spacefilled to 3.5 Å^[4]).

Most of the large cavity is filled by domains D0 and D1, but these domains are missing in this model.

Each of the 11 protofilaments has a distinct color, so there are 11 colors. Here, . Each protofilament forms one of the 11-start helices.

There is a large space between domains D2+D3 within a protofilament. Thus, protofilaments are held together by interactions between D0 and D1 (missing in this model). However, domains D2+D3 interact between protofilaments, forming 6 helices. Here, .

Black line: one of the 11-start protofilament helices.

Red line: one of the 6-start helices.

Notes and References

↑ Kido Y, Yoon YH, Samatey FA. Crystallization of a 79 kDa fragment of the hook protein FlgE from Campylobacter jejuni. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt, 12):1653-7. Epub 2011 Nov 30. PMID:22139190 doi:10.1107/S1744309111043272
↑ Brenner FW, Villar RG, Angulo FJ, Tauxe R, Swaminathan B. Salmonella nomenclature. J Clin Microbiol. 2000 Jul;38(7):2465-7. PMID:10878026
↑ Wagenknecht T, DeRosier D, Shapiro L, Weissborn A. Three-dimensional reconstruction of the flagellar hook from Caulobacter crescentus. J Mol Biol. 1981 Sep 25;151(3):439-65. PMID:7338902 doi:http://dx.doi.org/10.1016/0022-2836(81)90005-X
↑ The Caulobacter crecentus hook model contains 55 copies of the monomer, for a total of 121,055 non-hydrogen atoms. There are 16,665 alpha carbon atoms in the model. The van der Waals radius of carbon is 1.7 Å. In order to make the FlgE domains look solid, the alpha carbons are displayed with a radius of 3.5 Å.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

Retrieved from "http://52.214.119.220/wiki/index.php/User:Fadel_A._Samatey/FlgE_I"

@@ Line 101: / Line 101: @@
 Each of the 11 protofilaments has a distinct color, so there are 11 colors. Here, <scene name='47/478822/Caucr-hook-cao/2'>one protofilament is marked with a black line</scene>. Each protofilament forms one of the 11-start helices.
-There is a large space between domains D2+D3 '''within''' a protofilament. Thus, protofilaments are held together by interactions between D0 and D1 (missing in this model). However, domains D2+D3 interact '''between''' protofilaments, forming 6 helices. Here, <scene name='47/478822/Caucr-hook-cao/3'>one of the 6-start helices is marked with a red line, and the 6 starts are numbered</scene>.
+There is a large space between domains D2+D3 '''within''' a protofilament. Thus, protofilaments are held together by interactions between D0 and D1 (missing in this model). However, domains D2+D3 interact '''between''' protofilaments, forming 6 helices. Here, <scene name='47/478822/Caucr-hook-cao/3'>one of the 6-start helices is marked with a red line, and the 6 starts are numbered</scene>.<b>
+*Black line: one of the 11-start protofilament helices. <font color="red">
+*Red line: one of the 6-start helices.</font></b>
 <hr>
 </StructureSection>

User:Fadel A. Samatey/FlgE I

From Proteopedia

Revision as of 11:41, 20 October 2016

Molecular Tour

Contents

Monomer Structures

Campylobacter jejuni

Caulobacter crescentus

Comparison with Salmonella

Caulobacter Hook Model

Notes and References

Proteopedia Page Contributors and Editors (what is this?)

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