1yu3: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1yu3.png|left|200px]]
-<!--
+==Major Tropism Determinant I1 Variant==
-The line below this paragraph, containing "STRUCTURE_1yu3", creates the "Structure Box" on the page.
+<StructureSection load='1yu3' size='340' side='right'caption='[[1yu3]], [[Resolution|resolution]] 2.52&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'>[[1yu3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_phage_BIP-1 Bordetella phage BIP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YU3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YU3 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]] 2.52&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_1yu3|  PDB=1yu3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yu3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yu3 OCA], [https://pdbe.org/1yu3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yu3 RCSB], [https://www.ebi.ac.uk/pdbsum/1yu3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yu3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FIBD_BPBPP FIBD_BPBPP] Tail fiber protein located at the distal ends of the fibers that binds to the adhesion receptors on the host surface, thereby determining the host range. The phage can alter its tropism by modifying this protein. Variants are expressed through a diversity-generating retroelement (DGR) that creates mutant copies of a template repeat and replaces the end of the tail fiber receptor-binding protein with these sequences, thus changing the host range. Milliards of variants of the fiber receptor-binding protein can be created with this system.<ref>PMID:15386016</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Only few instances are known of protein folds that tolerate massive sequence variation for the sake of binding diversity. The most extensively characterized is the immunoglobulin fold. We now add to this the C-type lectin (CLec) fold, as found in the major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein of Bordetella bacteriophage. Variation in Mtd, with its approximately 10(13) possible sequences, enables phage adaptation to Bordetella spp. Mtd is an intertwined, pyramid-shaped trimer, with variable residues organized by its CLec fold into discrete receptor-binding sites. The CLec fold provides a highly static scaffold for combinatorial display of variable residues, probably reflecting a different evolutionary solution for balancing diversity against stability from that in the immunoglobulin fold. Mtd variants are biased toward the receptor pertactin, and there is evidence that the CLec fold is used broadly for sequence variation by related retroelements.
-===Major Tropism Determinant I1 Variant===
+The C-type lectin fold as an evolutionary solution for massive sequence variation.,McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P Nat Struct Mol Biol. 2005 Oct;12(10):886-92. Epub 2005 Sep 18. PMID:16170324<ref>PMID:16170324</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16170324}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1yu3" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16170324 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16170324}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bordetella phage BIP-1]]
-YU3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YU3 OCA].
+[[Category: Large Structures]]
+[[Category: Ghosh P]]
-==Reference==
+[[Category: Lawton JA]]
-The C-type lectin fold as an evolutionary solution for massive sequence variation., McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P, Nat Struct Mol Biol. 2005 Oct;12(10):886-92. Epub 2005 Sep 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16170324 16170324]
+[[Category: McMahon SA]]
-[[Category: Single protein]]
+[[Category: Miller JL]]
-[[Category: Viruses]]
-[[Category: Ghosh, P.]]
-[[Category: Lawton, J A.]]
-[[Category: McMahon, S A.]]
-[[Category: Miller, J L.]]
-[[Category: Beta prism]]
-[[Category: Beta sandwich]]
-[[Category: C-type lectin]]
-[[Category: Diversity-generating retroelement]]
-[[Category: Variability]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:23:46 2008''