6jk5: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 6jk5 is ~~ON HOLD until Paper~~ Publication

==Ca2+-dependent type II antifreeze protein (Ca2+-free form)==

== Structural highlights ==

<table><tr><td colspan='2'>[[6jk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hypomesus_nipponensis Hypomesus nipponensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JK5 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25Å</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>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6jk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jk5 OCA], [https://pdbe.org/6jk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jk5 RCSB], [https://www.ebi.ac.uk/pdbsum/6jk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jk5 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/P84493_9TELE P84493_9TELE]

== Publication Abstract from PubMed ==

Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca(2+)-dependent species of AFP, however, it has not been clarified how 1 mol of Ca(2+)-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca(2+)-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca(2+)-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Calpha = 0.31 A), while they exhibited a significant difference around their Ca(2+)-binding site. Firstly, the side-chains of four of the five Ca(2+)-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca(2+)-bound state. Second, a Ca(2+)-binding loop consisting of a segment D94-E99 becomes less flexible by the Ca(2+)-binding. Third, the Ca(2+)-binding induces a generation of ice-like clathrate waters around the Ca(2+)-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca(2+)-binding enables the ice-binding of this protein.

~~Authors:~~ Arai, T., ~~Tsuda~~, S., Kondo, H.~~, Nishimiya, Y~~.

Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface.,Arai T, Nishimiya Y, Ohyama Y, Kondo H, Tsuda S Biomolecules. 2019 Apr 27;9(5). pii: biom9050162. doi: 10.3390/biom9050162. PMID:31035615<ref>PMID:31035615</ref>

~~Description~~: ~~Ca2+-dependent type II antifreeze~~ protein ~~(Ca2+-free form)~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Kondo, H~~]]

[[Category: ~~Nishimiya, Y~~]]

[[Category: ~~Tsuda, S~~]]

==See Also==

[[Category: ~~Arai, T~~]]

*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]

== References ==

__TOC__

</StructureSection>

[[Category: Hypomesus nipponensis]]

[[Category: Large Structures]]

[[Category: Arai T]]

[[Category: Kondo H]]

[[Category: Nishimiya Y]]

[[Category: Tsuda S]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6jk5 is ON HOLD  until Paper Publication
+==Ca2+-dependent type II antifreeze protein (Ca2+-free form)==
+<StructureSection load='6jk5' size='340' side='right'caption='[[6jk5]], [[Resolution|resolution]] 1.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6jk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hypomesus_nipponensis Hypomesus nipponensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JK5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.25&#8491;</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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6jk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jk5 OCA], [https://pdbe.org/6jk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jk5 RCSB], [https://www.ebi.ac.uk/pdbsum/6jk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jk5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/P84493_9TELE P84493_9TELE]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hydration is crucial for a function and a ligand recognition of a protein. The hydration shell constructed on an antifreeze protein (AFP) contains many organized waters, through which AFP is thought to bind to specific ice crystal planes. For a Ca(2+)-dependent species of AFP, however, it has not been clarified how 1 mol of Ca(2+)-binding is related with the hydration and the ice-binding ability. Here we determined the X-ray crystal structure of a Ca(2+)-dependent AFP (jsAFP) from Japanese smelt, Hypomesus nipponensis, in both Ca(2+)-bound and -free states. Their overall structures were closely similar (Root mean square deviation (RMSD) of Calpha = 0.31 A), while they exhibited a significant difference around their Ca(2+)-binding site. Firstly, the side-chains of four of the five Ca(2+)-binding residues (Q92, D94 E99, D113, and D114) were oriented to be suitable for ice binding only in the Ca(2+)-bound state. Second, a Ca(2+)-binding loop consisting of a segment D94-E99 becomes less flexible by the Ca(2+)-binding. Third, the Ca(2+)-binding induces a generation of ice-like clathrate waters around the Ca(2+)-binding site, which show a perfect position-match to the waters constructing the first prism plane of a single ice crystal. These results suggest that generation of ice-like clathrate waters induced by Ca(2+)-binding enables the ice-binding of this protein.
-Authors: Arai, T., Tsuda, S., Kondo, H., Nishimiya, Y.
+Calcium-Binding Generates the Semi-Clathrate Waters on a Type II Antifreeze Protein to Adsorb onto an Ice Crystal Surface.,Arai T, Nishimiya Y, Ohyama Y, Kondo H, Tsuda S Biomolecules. 2019 Apr 27;9(5). pii: biom9050162. doi: 10.3390/biom9050162. PMID:31035615<ref>PMID:31035615</ref>
-Description: Ca2+-dependent type II antifreeze protein (Ca2+-free form)
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Kondo, H]]
+<div class="pdbe-citations 6jk5" style="background-color:#fffaf0;"></div>
-[[Category: Nishimiya, Y]]
-[[Category: Tsuda, S]]
+==See Also==
-[[Category: Arai, T]]
+*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Hypomesus nipponensis]]
+[[Category: Large Structures]]
+[[Category: Arai T]]
+[[Category: Kondo H]]
+[[Category: Nishimiya Y]]
+[[Category: Tsuda S]]