1wrf: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (15 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
== | ==Refined solution structure of Der f 2, The Major Mite Allergen from Dermatophagoides farinae== | ||
<StructureSection load='1wrf' size='340' side='right'caption='[[1wrf]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1wrf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dermatophagoides_farinae Dermatophagoides farinae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WRF FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 11 models</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wrf OCA], [https://pdbe.org/1wrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wrf RCSB], [https://www.ebi.ac.uk/pdbsum/1wrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wrf ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ALL2_DERFA ALL2_DERFA] | |||
== 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/wr/1wrf_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=1wrf ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Group 2 major mite allergens Der f 2 and Der p 2 are classified into the recently identified group of MD-2-related lipid-recognition (ML) proteins, but the ligands and biological functions of these allergens are unknown. We have obtained a high-quality NMR structure for Der f 2, and found that it is more similar to the crystal structure of NPC2, a distant homologue, than to that of Der p 2, in terms of the separation and angle between the two major beta-sheets. This made us propose that ML proteins undergo clamshell-like motions that change the sizes of ligand-binding spaces inside their immunoglobulin-fold beta-sandwich to accommodate lipid molecules. This type of motion in lipopolysaccaride recognition of MD-2 is suggested to be likely as well by structural models. We also report the applicability of NMR differential exchange broadening experiments for complexes of intact monoclonal antibodies and antigens; using this technique, we have detected the conformational epitopes for monoclonal antibodies 15E11 and 13A4 as two separate surface patches. | Group 2 major mite allergens Der f 2 and Der p 2 are classified into the recently identified group of MD-2-related lipid-recognition (ML) proteins, but the ligands and biological functions of these allergens are unknown. We have obtained a high-quality NMR structure for Der f 2, and found that it is more similar to the crystal structure of NPC2, a distant homologue, than to that of Der p 2, in terms of the separation and angle between the two major beta-sheets. This made us propose that ML proteins undergo clamshell-like motions that change the sizes of ligand-binding spaces inside their immunoglobulin-fold beta-sandwich to accommodate lipid molecules. This type of motion in lipopolysaccaride recognition of MD-2 is suggested to be likely as well by structural models. We also report the applicability of NMR differential exchange broadening experiments for complexes of intact monoclonal antibodies and antigens; using this technique, we have detected the conformational epitopes for monoclonal antibodies 15E11 and 13A4 as two separate surface patches. | ||
NMR study on the major mite allergen Der f 2: its refined tertiary structure, epitopes for monoclonal antibodies and characteristics shared by ML protein group members.,Ichikawa S, Takai T, Inoue T, Yuuki T, Okumura Y, Ogura K, Inagaki F, Hatanaka H J Biochem. 2005 Mar;137(3):255-63. PMID:15809326<ref>PMID:15809326</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1wrf" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Dermatophagoides farinae]] | [[Category: Dermatophagoides farinae]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Hatanaka | [[Category: Hatanaka H]] | ||
[[Category: Ichikawa | [[Category: Ichikawa S]] | ||
[[Category: Inagaki | [[Category: Inagaki F]] | ||
[[Category: Inoue | [[Category: Inoue T]] | ||
[[Category: Ogura | [[Category: Ogura K]] | ||
[[Category: Okumura | [[Category: Okumura Y]] | ||
[[Category: Takai | [[Category: Takai T]] | ||
[[Category: Yuuki | [[Category: Yuuki T]] | ||
Latest revision as of 07:42, 23 October 2024
Refined solution structure of Der f 2, The Major Mite Allergen from Dermatophagoides farinae
| ||||||||||||
