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5xqn

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Current revision (10:19, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5xqn' size='340' side='right'caption='[[5xqn]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
<StructureSection load='5xqn' size='340' side='right'caption='[[5xqn]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5xqn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Enchelyopus_elongatus Enchelyopus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XQN FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5xqn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoarces_elongatus Zoarces elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XQN FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.19&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqn OCA], [http://pdbe.org/5xqn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqn RCSB], [http://www.ebi.ac.uk/pdbsum/5xqn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqn ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5xqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqn OCA], [https://pdbe.org/5xqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xqn RCSB], [https://www.ebi.ac.uk/pdbsum/5xqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqn ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/Q53UJ4_9TELE Q53UJ4_9TELE]] Lowers the blood freezing point. Contributes to protect fish blood from freezing at subzero sea water temperatures. Binds to nascent ice crystals and prevents further growth.[RuleBase:RU362061]
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[https://www.uniprot.org/uniprot/Q53UJ4_9TELE Q53UJ4_9TELE] Lowers the blood freezing point. Contributes to protect fish blood from freezing at subzero sea water temperatures. Binds to nascent ice crystals and prevents further growth.[RuleBase:RU362061]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in ice-binding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of approximately 50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the [Formula: see text] first prism plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the [Formula: see text] pyramidal ice plane. The order of ice-binding strength was A20L &lt; A20G &lt; WT &lt; A20T &lt; A20V &lt; A20I, where the top three mutants capable of binding to the first prism and the pyramidal ice planes commonly contained a bifurcated gamma-CH3 group. These results suggest that a fine-tuning of the surface of Zoarcidae-derived IBP assisted by a side-chain group regulates the holding property of its polypentagonal water network, the function of which is to freeze the host protein to specific ice planes.
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Polypentagonal ice-like water networks emerge solely in an activity-improved variant of ice-binding protein.,Mahatabuddin S, Fukami D, Arai T, Nishimiya Y, Shimizu R, Shibazaki C, Kondo H, Adachi M, Tsuda S Proc Natl Acad Sci U S A. 2018 May 7. pii: 1800635115. doi:, 10.1073/pnas.1800635115. PMID:29735675<ref>PMID:29735675</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5xqn" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Enchelyopus elongatus]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Adachi, M]]
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[[Category: Zoarces elongatus]]
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[[Category: Kondo, H]]
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[[Category: Adachi M]]
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[[Category: Tsuda, S]]
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[[Category: Kondo H]]
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[[Category: Antifreeze protein]]
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[[Category: Tsuda S]]
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[[Category: Notched-fin eelpout]]
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[[Category: Type iii]]
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Current revision

Crystal structure of Notched-fin eelpout type III antifreeze protein (NFE6, AFP), C2221 form.

PDB ID 5xqn

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