1ucs

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(New page: 200px<br /><applet load="1ucs" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ucs, resolution 0.62&Aring;" /> '''Type III Antifreeze ...)
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[[Image:1ucs.jpg|left|200px]]<br /><applet load="1ucs" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ucs, resolution 0.62&Aring;" />
 
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'''Type III Antifreeze Protein RD1 from an Antarctic Eel Pout'''<br />
 
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==Overview==
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==Type III Antifreeze Protein RD1 from an Antarctic Eel Pout==
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RD1 is a 7-kDa globular protein from the Antarctic eel pout Lycodichthys, dearborni. It belongs to type III of the four types of antifreeze proteins, (AFPs) found in marine fishes living at subzero temperatures. For type III, AFP, a potential ice-binding flat surface has been identified and is, imbedded with side chains capable of making hydrogen bonds with a specific, lattice plane on ice. So far, all crystallographic studies on type III, AFPs were carried out using the Atlantic ocean pout Macrozoarces, americanus as the source organism. Here we present the crystal structure, of a type III AFP from a different zoarcid fish, and at an ultra-high, resolution of 0.62 A. The protein fold of RD1 comprises a compact globular, domain with two internal tandem motifs arranged about a pseudo-dyad, symmetry. Each motif of the "pretzel fold" includes four short, beta-strands and a 3(10) helix. There is a novel internal cavity of 45, A(3) surrounded by eight conserved nonpolar residues. The model contains, several residues with alternate conformations, and a number of split water, molecules, probably caused by alternate interactions with the protein, molecule. After extensive refinement that includes hydrogen atoms, significant residual electron densities associated with the electrons of, peptides and many other bonds could be visualized.
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<StructureSection load='1ucs' size='340' side='right'caption='[[1ucs]], [[Resolution|resolution]] 0.62&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ucs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lycodichthys_dearborni Lycodichthys dearborni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UCS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UCS FirstGlance]. <br>
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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]] 0.62&#8491;</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=1ucs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ucs OCA], [https://pdbe.org/1ucs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ucs RCSB], [https://www.ebi.ac.uk/pdbsum/1ucs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ucs ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ANP1_LYCDA ANP1_LYCDA] Contributes to protect fish blood from freezing at subzero sea water temperatures. Lowers the blood freezing point. Binds to nascent ice crystals and prevents further growth (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uc/1ucs_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ucs ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1UCS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lycodichthys_dearborni Lycodichthys dearborni]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UCS OCA].
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*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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The refined crystal structure of an eel pout type III antifreeze protein RD1 at 0.62-A resolution reveals structural microheterogeneity of protein and solvation., Ko TP, Robinson H, Gao YG, Cheng CH, DeVries AL, Wang AH, Biophys J. 2003 Feb;84(2 Pt 1):1228-37. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12547803 12547803]
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[[Category: Large Structures]]
[[Category: Lycodichthys dearborni]]
[[Category: Lycodichthys dearborni]]
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[[Category: Single protein]]
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[[Category: Cheng C-HC]]
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[[Category: Cheng, C.H.C.]]
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[[Category: DeVries AL]]
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[[Category: DeVries, A.L.]]
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[[Category: Gao Y-G]]
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[[Category: Gao, Y.G.]]
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[[Category: Ko T-P]]
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[[Category: Ko, T.P.]]
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[[Category: Robinson H]]
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[[Category: Robinson, H.]]
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[[Category: Wang AH-J]]
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[[Category: Wang, A.H.J.]]
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[[Category: pretzel fold]]
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[[Category: small beta barrel]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:01:34 2007''
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Current revision

Type III Antifreeze Protein RD1 from an Antarctic Eel Pout

PDB ID 1ucs

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