2h8f: Difference between revisions

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-[[Image:2h8f.png|left|200px]]
-<!--
+==Crystal structure of deoxy hemoglobin from Trematomus bernacchii at pH 6.2==
-The line below this paragraph, containing "STRUCTURE_2h8f", creates the "Structure Box" on the page.
+<StructureSection load='2h8f' size='340' side='right'caption='[[2h8f]], [[Resolution|resolution]] 1.30&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'>[[2h8f]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trematomus_bernacchii Trematomus bernacchii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H8F 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]] 1.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-{{STRUCTURE_2h8f|  PDB=2h8f  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2h8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h8f OCA], [https://pdbe.org/2h8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h8f RCSB], [https://www.ebi.ac.uk/pdbsum/2h8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h8f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HBA_TREBE HBA_TREBE] Involved in oxygen transport from gills to the various peripheral tissues.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h8/2h8f_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2h8f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Root effect is a widespread property in fish hemoglobins (Hbs) that produces a drastic reduction of cooperativity and oxygen-binding ability at acidic pH. Here, we report the high-resolution structure of the deoxy form of Hb isolated from the Antarctic fish Trematomus bernacchii (HbTb) crystallized at pH 6.2 and 8.4. The structure at acidic pH has been previously determined at a moderate resolution (Ito et al., J Mol Biol 1995;250:648-658). Our results provide a clear picture of the events occurring upon the pH increase from 6.2 to 8.4, observed within a practically unchanged crystal environment. In particular, at pH 8.4, the interaspartic hydrogen bond at the alpha(1)beta(2) interface is partially broken, suggesting a pK(a) close to 8.4 for Asp95alpha. In addition, a detailed survey of the histidine modifications, caused by the change in pH, also indicates that at least three hot regions of the molecule are modified (Ebeta helix, Cbeta-tail, CDalpha corner) and can be considered to be involved at various levels in the release of the Root protons. Most importantly, at the CDalpha corner, the break of the salt bridge Asp48alpha-His55alpha allows us to describe a detailed mechanism that transmits the modification from the CDalpha corner far to the alpha heme. More generally, the results shed light on the role played by the histidine residues in modulating the strength of the Root effect and also support the emerging idea that the structural determinants, at least for a part of the Root effect, are specific of each Hb endowed with this property.
-===Crystal structure of deoxy hemoglobin from Trematomus bernacchii at pH 6.2===
+High resolution crystal structure of deoxy hemoglobin from Trematomus bernacchii at different pH values: the role of histidine residues in modulating the strength of the root effect.,Mazzarella L, Vergara A, Vitagliano L, Merlino A, Bonomi G, Scala S, Verde C, di Prisco G Proteins. 2006 Nov 1;65(2):490-8. PMID:16909420<ref>PMID:16909420</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_16909420}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2h8f" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16909420 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16909420}}
-==About this Structure==
-[[2h8f]] is a 4 chain structure of [[Hemoglobin]] with sequence from [http://en.wikipedia.org/wiki/Trematomus_bernacchii Trematomus bernacchii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H8F OCA].
 ==See Also==
-*[[Hemoglobin]]
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:16909420</ref><ref group="xtra">PMID:16299734</ref><ref group="xtra">PMID:10222199</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Trematomus bernacchii]]
-[[Category: Bonomi, G.]]
+[[Category: Bonomi G]]
-[[Category: Mazzarella, L.]]
+[[Category: Mazzarella L]]
-[[Category: Merlino, A.]]
+[[Category: Merlino A]]
-[[Category: Prisco, G di.]]
+[[Category: Scala S]]
-[[Category: Scala, S.]]
+[[Category: Verde C]]
-[[Category: Verde, C.]]
+[[Category: Vergara A]]
-[[Category: Vergara, A.]]
+[[Category: Vitagliano L]]
-[[Category: Vitagliano, L.]]
+[[Category: Di Prisco G]]
-[[Category: Allostery]]
-[[Category: Cooperativity]]
-[[Category: Hemoglobin]]
-[[Category: High resolution]]
-[[Category: Ph]]
-[[Category: Root effect]]
-[[Category: Transport protein]]