2d2m

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{{Seed}}
 
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[[Image:2d2m.png|left|200px]]
 
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==Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi==
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The line below this paragraph, containing "STRUCTURE_2d2m", creates the "Structure Box" on the page.
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<StructureSection load='2d2m' size='340' side='right'caption='[[2d2m]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2d2m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. The March 2013 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Erythrocruorin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2013_3 10.2210/rcsb_pdb/mom_2013_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2M 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]] 2.85&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
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{{STRUCTURE_2d2m| PDB=2d2m | SCENE= }}
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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=2d2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2m OCA], [https://pdbe.org/2d2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2m RCSB], [https://www.ebi.ac.uk/pdbsum/2d2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2m ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GLBA1_OLIMA GLBA1_OLIMA] The extracellular giant hemoglobin is able to bind and transport oxygen and hydrosulfide simultaneously and reversibly at two different sites.
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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/d2/2d2m_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2d2m ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.
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===Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi===
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Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.,Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14521-6. Epub 2005 Oct 3. PMID:16204001<ref>PMID:16204001</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2d2m" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16204001}}, adds the Publication Abstract to the page
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*[[Carbonic anhydrase 3D structures|Carbonic anhydrase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16204001 is the PubMed ID number.
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*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
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== References ==
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{{ABSTRACT_PUBMED_16204001}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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2D2M is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Oligobrachia_mashikoi Oligobrachia mashikoi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2M OCA].
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[[Category: Erythrocruorin]]
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[[Category: Large Structures]]
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==Reference==
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Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi., Numoto N, Nakagawa T, Kita A, Sasayama Y, Fukumori Y, Miki K, Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14521-6. Epub 2005 Oct 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16204001 16204001]
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[[Category: Oligobrachia mashikoi]]
[[Category: Oligobrachia mashikoi]]
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[[Category: Protein complex]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Fukumori, Y.]]
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[[Category: Fukumori Y]]
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[[Category: Kita, A.]]
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[[Category: Kita A]]
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[[Category: Miki, K.]]
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[[Category: Miki K]]
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[[Category: Nakagawa, T.]]
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[[Category: Nakagawa T]]
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[[Category: Numoto, N.]]
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[[Category: Numoto N]]
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[[Category: Sasayama, Y.]]
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[[Category: Sasayama Y]]
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[[Category: Giant hemoglobin]]
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[[Category: Invertebrate]]
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[[Category: Oligobrachia mashikoi]]
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[[Category: Pogonophora]]
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[[Category: Sulfide binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 12:18:34 2008''
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Current revision

Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi

PDB ID 2d2m

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