2ntf: Difference between revisions

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-{{Seed}}
-[[Image:2ntf.png|left|200px]]
-<!--
+==Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog==
-The line below this paragraph, containing "STRUCTURE_2ntf", creates the "Structure Box" on the page.
+<StructureSection load='2ntf' size='340' side='right'caption='[[2ntf]], [[Resolution|resolution]] 3.18&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ntf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NTF FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.18&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OHM:3-OXO-N-[(3S)-2-OXOPYRROLIDIN-3-YL]DODECANAMIDE'>OHM</scene></td></tr>
-{{STRUCTURE_2ntf|  PDB=2ntf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ntf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ntf OCA], [https://pdbe.org/2ntf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ntf RCSB], [https://www.ebi.ac.uk/pdbsum/2ntf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ntf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q99LC4_MOUSE Q99LC4_MOUSE]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nt/2ntf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ntf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A large number of Gram-negative bacteria employ N-acyl homoserine lactones (AHLs) as signaling molecules in quorum sensing, which is a population density-dependent mechanism to coordinate gene expression. Antibody RS2-1G9 was elicited against a lactam mimetic of the N-acyl homoserine lactone and represents the only reported monoclonal antibody that recognizes the naturally-occuring N-acyl homoserine lactone with high affinity. Due to its high cross-reactivity, RS2-1G9 showed remarkable inhibition of quorum sensing signaling in Pseudomonas aeruginosa, a common opportunistic pathogen in humans. The crystal structure of Fab RS2-1G9 in complex with a lactam analog revealed complete encapsulation of the polar lactam moiety in the antibody-combining site. This mode of recognition provides an elegant immunological solution for tight binding to an aliphatic, lipid-like ligand with a small head group lacking typical haptenic features, such as aromaticity or charge, which are often incorporated into hapten design to generate high-affinity antibodies. The ability of RS2-1G9 to discriminate between closely related AHLs is conferred by six hydrogen bonds to the ligand. Conversely, cross-reactivity of RS2-1G9 towards the lactone is likely to originate from conservation of these hydrogen bonds as well as an additional hydrogen bond to the oxygen of the lactone ring. A short, narrow tunnel exiting at the protein surface harbors a portion of the acyl chain and would not allow entry of the head group. The crystal structure of the antibody without its cognate lactam or lactone ligands revealed a considerably altered antibody-combining site with a closed binding pocket. Curiously, a completely buried ethylene glycol molecule mimics the lactam ring and, thus, serves as a surrogate ligand. The detailed structural delineation of this quorum-quenching antibody will aid further development of an antibody-based therapy against bacterial pathogens by interference with quorum sensing.
-===Crystal Structure of a Quorum-Quenching Antibody in Complex with an N-Acyl-L-Homoserine Lactone Analog===
+Crystal structures of a quorum-quenching antibody.,Debler EW, Kaufmann GF, Kirchdoerfer RN, Mee JM, Janda KD, Wilson IA J Mol Biol. 2007 May 18;368(5):1392-402. Epub 2007 Mar 6. PMID:17400249<ref>PMID:17400249</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ntf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17400249}}, adds the Publication Abstract to the page
+*[[Antibody 3D structures|Antibody 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17400249 is the PubMed ID number.
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
--->
+== References ==
-{{ABSTRACT_PUBMED_17400249}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NTF OCA].
+[[Category: Large Structures]]
+[[Category: Mus musculus]]
-==Reference==
+[[Category: Debler EW]]
-Crystal structures of a quorum-quenching antibody., Debler EW, Kaufmann GF, Kirchdoerfer RN, Mee JM, Janda KD, Wilson IA, J Mol Biol. 2007 May 18;368(5):1392-402. Epub 2007 Mar 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17400249 17400249]
+[[Category: Wilson IA]]
-[[Category: Debler, E W.]]
-[[Category: Wilson, I A.]]
-[[Category: Antibody]]
-[[Category: Fab]]
-[[Category: Hapten complex]]
-[[Category: Homoserine lactone]]
-[[Category: Immunoglobulin]]
-[[Category: Quorum sensing]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:20:28 2008''