User:Fadel A. Samatey/FlhBc I
From Proteopedia
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| - | + | [[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]] | |
| + | [[Image:Acta_Cryst_D.png|900 px]] | ||
| + | <br><br> | ||
| + | <span style="font-size:160%"><b>Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins.</b></span><br><br> | ||
| + | <span style="font-size:120%">Vladimir A. Meshcheryakov, Akio Kitao, Hideyuki Matsunami and Fadel A. Samatey. ''Acta Cryst. D69: 812-820 (2013). [http://dx.doi.org/10.1107/S0907444913002102 doi:10.1107/S0907444913002102]</span> | ||
| + | |||
| + | ===Brief Introduction=== | ||
| + | |||
| + | FlhB is a membrane protein that is part of the flagellum-specific secretion apparatus. It is required for secretion of flagellar proteins, and for bacterial motility. FlhB is paralogous to a protein in the virulence type III secretion system. | ||
| + | (Please see [http://dx.doi.org/10.1107/S0907444913002102 the publication] for a more detailed introduction.) | ||
| + | |||
| + | ==Molecular Tour: FlhBc Structures== | ||
| + | <StructureSection size='450' frame='true' align='right' caption='Cytoplasmic domain of FlhB' scene='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6' > | ||
| + | ====''Salmonella''==== | ||
| + | FlhB from ''Salmonella typhimurium'' consists of 383 amino acids. The cytoplasmic domain 219-383 (length 165, 43% of full length) was crystallized. The resulting model [[3b0z]] includes coordinates for residues 229-353 (length 125, 76% of the crystallized length). The [[asymmetric unit]] contains a single molecule (<scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st/6'>restore initial scene</scene>). As explained in the publication, the position of the long alpha helix appears to be stabilized by | ||
| + | crystal contacts (not shown). | ||
| + | <!--<scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st_xtl_contacts/2'>crystal contacts</scene> (use the ''popup'' button to see details).--> | ||
| + | |||
| + | The chain is <scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Cleavage/1'>cleaved at NPTH between Asn269 and Pro270</scene>. This is believed to be autocatalytic cleavage involved in the transition of the export apparatus from hook to filament mode. | ||
| + | |||
| + | ====''Aquifex''==== | ||
| + | FlhB from the thermophile<ref>[http://en.wikipedia.org/wiki/Aquifex_aeolicus Optimum growth ~90<sup>o</sup> C].</ref> ''Aquifex aeolicus'' is shorter, 350 residues (vs. 383 for ''S. typhimurium''), with 32% sequence identity. Residues 213-350 (length 138) were crystallized, and the resulting model [[3b1s]] has three molecules in the [[asymmetric unit]]. The molecule displayed here, with chains designated C and D, was chosen because it has the lowest average [[temperature factor]] (66.2, vs. 84.7 and 72.6 for A,B and E,F respectively). It has coordinates for 232-337 (length 106, 77% of the crystallized segment), cleaved at NPTH between Asn263 and Pro264. | ||
| + | |||
| + | ====Comparison==== | ||
| + | The FlhBc ''Salmonella'' <scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhb_st_aa_aligned/2'>3D structure is very similar</scene> to that of ''Aquifex''. Their FlhB's have 32% sequence identity. | ||
| + | <!-- compare does not exist in Jmol 11.8; the code below can become active after Jmol is upgraded to 12.2. | ||
| + | <scene name='User:Fadel_A._Samatey/Workbench/I3DC-1/Flhbc_st_plus_aa/2'>Display both structures</scene>, then click the button below to do a structural alignment. | ||
| + | <jmol> | ||
| + | <jmolButton> | ||
| + | <script>if (~flbstaa); compare {1.1} {1.2} SUBSET {*.ca} {246-269:A} {240-263:C} {272-280:B} {266-274:D} {285-351:B} {279-345:D} ATOMS rotate translate; zoomto *1.4; else; set echo bottom left; color echo white; font echo 20 sansserif;echo "Please display both structures first!"; delay 4; set echo off; endif;</script> | ||
| + | <text>Do Structural Alignment</text> | ||
| + | </jmolButton> | ||
| + | </jmol> | ||
| + | --> | ||
| + | </StructureSection> | ||
| + | ===References and Notes=== | ||
| + | <references /> | ||
| + | |||
| + | ===Notes for Developers=== | ||
| + | *[[Image:Workbench 3b0z.pdb.gz]] | ||
| + | *[[Image:Workbench 3b1s.pdb.gz]] | ||
| + | *[[Image:Workbench 3b0z 3b1sCD.pdb]] 1.1 is 3b0z(St) while 1.2 is 3b1s chains C and D. Not aligned. | ||
| + | *[[Image:Workbench 3b0z 3b1sCD aligned.pdb]] | ||
| + | __NOTOC__ <!-- NOTOC suppresses display of a Table of Contents --> | ||
Revision as of 09:08, 29 April 2013
Interactive 3D Complement in Proteopedia
Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins.
Vladimir A. Meshcheryakov, Akio Kitao, Hideyuki Matsunami and Fadel A. Samatey. Acta Cryst. D69: 812-820 (2013). doi:10.1107/S0907444913002102
Brief Introduction
FlhB is a membrane protein that is part of the flagellum-specific secretion apparatus. It is required for secretion of flagellar proteins, and for bacterial motility. FlhB is paralogous to a protein in the virulence type III secretion system. (Please see the publication for a more detailed introduction.)
Molecular Tour: FlhBc Structures
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References and Notes
Notes for Developers
- Image:Workbench 3b0z.pdb.gz
- Image:Workbench 3b1s.pdb.gz
- Image:Workbench 3b0z 3b1sCD.pdb 1.1 is 3b0z(St) while 1.2 is 3b1s chains C and D. Not aligned.
- Image:Workbench 3b0z 3b1sCD aligned.pdb
