1ith: Difference between revisions

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-[[Image:1ith.gif|left|200px]]<br /><applet load="1ith" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1ith, resolution 2.5&Aring;" />
-'''STRUCTURE DETERMINATION AND REFINEMENT OF HOMOTETRAMERIC HEMOGLOBIN FROM URECHIS CAUPO AT 2.5 ANGSTROMS RESOLUTION'''<br />
-==Overview==
+==STRUCTURE DETERMINATION AND REFINEMENT OF HOMOTETRAMERIC HEMOGLOBIN FROM URECHIS CAUPO AT 2.5 ANGSTROMS RESOLUTION==
-A 5 A resolution multiple isomorphous replacement solution for hemoglobin isolated from Urechis caupo revealed a previously unobserved quaternary structure for tetrameric hemoglobin [Kolatkar, Meador, Stanfield &amp; Hackert (1988). J. Biol. Chem. 263(7), 3462-3465]. We report here the structure of Urechis hemoglobin in the cyanomet state refined to 2.5 A resolution by simulated annealing yielding R = 0.148 for reflections F greater than 3 sigma between 5.0 and 2.5 A resolution. The starting model was fitted to a map originally derived from multiple-wavelength anomalous-dispersion phases to 3 A resolution that was then subjected to cyclic twofold molecular averaging and solvent flattening. Structural analysis of the resultant model shows that the unique quaternary assemblage is possible due to several favorable interactions between subunits, including salt links, hydrophobic pockets and interactions mediated by bound water. The tetramer is stabilized by subunit-subunit interactions between the G/H turns and D helices within the crystallographic dimer, and the A/B turn regions and E helices between subunits related by a molecular twofold axis. Interestingly, each subunit has one cysteine residue (Cys21) located in the A/B turn. These twofold-related cysteinyl residues are near enough to one another to form a disulfide bridge but do not.
+<StructureSection load='1ith' size='340' side='right'caption='[[1ith]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ith]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Urechis_caupo Urechis caupo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ITH 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1ith FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ith OCA], [https://pdbe.org/1ith PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ith RCSB], [https://www.ebi.ac.uk/pdbsum/1ith PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ith ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HBF1_URECA HBF1_URECA] Hemoglobin F-I appears to function in storage, rather than transport of oxygen.
+== 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/it/1ith_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1ith ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-ITH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Urechis_caupo Urechis caupo] with <scene name='pdbligand=CYN:'>CYN</scene> and <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ITH OCA].
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Structure determination and refinement of homotetrameric hemoglobin from Urechis caupo at 2.5 A resolution., Kolatkar PR, Ernst SR, Hackert ML, Ogata CM, Hendrickson WA, Merritt EA, Phizackerley RP, Acta Crystallogr B. 1992 Apr 1;48 ( Pt 2):191-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1515107 1515107]
+[[Category: Large Structures]]
-[[Category: Single protein]]
 [[Category: Urechis caupo]]
-[[Category: Ernst, S R.]]
+[[Category: Ernst SR]]
-[[Category: Hackert, M.]]
+[[Category: Hackert M]]
-[[Category: Hendrickson, W A.]]
+[[Category: Hendrickson WA]]
-[[Category: Kolatkar, P.]]
+[[Category: Kolatkar P]]
-[[Category: Merritt, E A.]]
+[[Category: Merritt EA]]
-[[Category: Ogata, C M.]]
+[[Category: Ogata CM]]
-[[Category: Phizackerley, R P.]]
+[[Category: Phizackerley RP]]
-[[Category: CYN]]
-[[Category: HEM]]
-[[Category: oxygen transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:15:30 2008''