3vn3: Difference between revisions

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-[[Image:3vn3.jpg|left|200px]]
-<!--
+==Fungal antifreeze protein exerts hyperactivity by constructing an inequable beta-helix==
-The line below this paragraph, containing "STRUCTURE_3vn3", creates the "Structure Box" on the page.
+<StructureSection load='3vn3' size='340' side='right'caption='[[3vn3]], [[Resolution|resolution]] 0.95&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'>[[3vn3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Typhula_ishikariensis Typhula ishikariensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VN3 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]] 0.95&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IYR:3-IODO-TYROSINE'>IYR</scene></td></tr>
-{{STRUCTURE_3vn3|  PDB=3vn3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vn3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vn3 OCA], [https://pdbe.org/3vn3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vn3 RCSB], [https://www.ebi.ac.uk/pdbsum/3vn3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vn3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IBPKB_TYPIS IBPKB_TYPIS] Binds to the surface of ice crystals. Has low thermal hysteresis (TH) activity, which is the ability to lower the freezing point of an aqueous solution below its melting point (PubMed:22645341). The TH activity of this protein is approximately 0.3 degrees Celsius at 11 mM (PubMed:27613857).<ref>PMID:22645341</ref> <ref>PMID:27613857</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Antifreeze proteins (AFPs) are found in organisms ranging from fish to bacteria, where they serve different functions to facilitate survival of their host. AFPs that protect freeze-intolerant fish and insects from internal ice growth bind to ice using a regular array of well-conserved residues/motifs. Less is known about the role of AFPs in freeze-tolerant species, which might be to beneficially alter the structure of ice in or around the host. Here we report the 0.95-A high-resolution crystal structure of a 223-residue secreted AFP from the snow mold fungus Typhula ishikariensis. Its main structural element is an irregular beta-helix with six loops of 18 or more residues that lies alongside an alpha-helix. beta-Helices have independently evolved as AFPs on several occasions and seem ideally structured to bind to several planes of ice, including the basal plane. A novelty of the beta-helical fold is the nonsequential arrangement of loops that places the N- and C termini inside the solenoid of beta-helical coils. The ice-binding site (IBS), which could not be predicted from sequence or structure, was located by site-directed mutagenesis to the flattest surface of the protein. It is remarkable for its lack of regularity and its poor conservation in homologs from psychrophilic diatoms and bacteria and other fungi.
-===Fungal antifreeze protein exerts hyperactivity by constructing an inequable beta-helix===
+Ice-binding site of snow mold fungus antifreeze protein deviates from structural regularity and high conservation.,Kondo H, Hanada Y, Sugimoto H, Hoshino T, Garnham CP, Davies PL, Tsuda S Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9360-5. Epub 2012 May 29. PMID:22645341<ref>PMID:22645341</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3vn3" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[3vn3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Typhula_ishikariensis Typhula ishikariensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VN3 OCA].
+*[[Antifreeze protein|Antifreeze protein]]
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Typhula ishikariensis]]
-[[Category: Davies, P L.]]
+[[Category: Davies PL]]
-[[Category: Garnham, C P.]]
+[[Category: Garnham CP]]
-[[Category: Hanada, Y.]]
+[[Category: Hanada Y]]
-[[Category: Hoshino, T.]]
+[[Category: Hoshino T]]
-[[Category: Kondo, H.]]
+[[Category: Kondo H]]
-[[Category: Sugimoto, H.]]
+[[Category: Sugimoto H]]
-[[Category: Tsuda, S.]]
+[[Category: Tsuda S]]
-[[Category: Xiao, N.]]
+[[Category: Xiao N]]
-[[Category: Antifreeze protein]]
-[[Category: Right-handed beta-helix]]