2dc3: Difference between revisions

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New page: left|200px<br /> <applet load="2dc3" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dc3, resolution 1.68Å" /> '''Crystal structure o...
 
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[[Image:2dc3.gif|left|200px]]<br />
<applet load="2dc3" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2dc3, resolution 1.68&Aring;" />
'''Crystal structure of human cytoglobin at 1.68 angstroms resolution'''<br />


==Overview==
==Crystal structure of human cytoglobin at 1.68 angstroms resolution==
Cytoglobin (Cgb) is a recently discovered member of the vertebrate, haem-containing globin family. The structure of a new crystal form of, wild-type human Cgb (space group C2) was determined at a resolution of, 1.68 Angstrom. The results show the presence of an additional helix in the, N-terminal residues (4-20) prior to the A helix and an ordered loop, structure in the C-terminal region (168-188), while these extended, peptides were invisible owing to disorder in the previously reported, structures using a P3(2)21 crystal at a resolution of 2.4 Angstrom. A, detailed comparison of the two crystal structures shows differences in the, conformation of the residues (i.e. Arg84) in the haem environment owing to, a different dimeric arrangement.
<StructureSection load='2dc3' size='340' side='right'caption='[[2dc3]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2dc3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DC3 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]] 1.68&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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=2dc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc3 OCA], [https://pdbe.org/2dc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dc3 RCSB], [https://www.ebi.ac.uk/pdbsum/2dc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc3 ProSAT], [https://www.topsan.org/Proteins/RSGI/2dc3 TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CYGB_HUMAN CYGB_HUMAN] May have a protective function during conditions of oxidative stress. May be involved in intracellular oxygen storage or transfer.
== 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/dc/2dc3_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=2dc3 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cytoglobin (Cgb) is a recently discovered member of the vertebrate haem-containing globin family. The structure of a new crystal form of wild-type human Cgb (space group C2) was determined at a resolution of 1.68 Angstrom. The results show the presence of an additional helix in the N-terminal residues (4-20) prior to the A helix and an ordered loop structure in the C-terminal region (168-188), while these extended peptides were invisible owing to disorder in the previously reported structures using a P3(2)21 crystal at a resolution of 2.4 Angstrom. A detailed comparison of the two crystal structures shows differences in the conformation of the residues (i.e. Arg84) in the haem environment owing to a different dimeric arrangement.


==About this Structure==
High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode.,Makino M, Sugimoto H, Sawai H, Kawada N, Yoshizato K, Shiro Y Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):671-7. Epub 2006, May 12. PMID:16699195<ref>PMID:16699195</ref>
2DC3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with HEM and ACY as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DC3 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
High-resolution structure of human cytoglobin: identification of extra N- and C-termini and a new dimerization mode., Makino M, Sugimoto H, Sawai H, Kawada N, Yoshizato K, Shiro Y, Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):671-7. Epub 2006, May 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16699195 16699195]
</div>
<div class="pdbe-citations 2dc3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Kawada, N.]]
[[Category: Kawada N]]
[[Category: Makino, M.]]
[[Category: Makino M]]
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
[[Category: Sawai H]]
[[Category: Sawai, H.]]
[[Category: Shiro Y]]
[[Category: Shiro, Y.]]
[[Category: Sugimoto H]]
[[Category: Sugimoto, H.]]
[[Category: Yoshizato K]]
[[Category: Yoshizato, K.]]
[[Category: ACY]]
[[Category: HEM]]
[[Category: cytoglobin]]
[[Category: heme]]
[[Category: myoglobin]]
[[Category: oxygen storage]]
[[Category: oxygen transport]]
[[Category: riken structural genomics/proteomics initiative]]
[[Category: rsgi]]
[[Category: structural genomics]]
 
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Retrieved from "https://proteopedia.org/2dc3"