1od5

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[[Image:1od5.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of glycinin A3B4 subunit homohexamer==
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|PDB= 1od5 |SIZE=350|CAPTION= <scene name='initialview01'>1od5</scene>, resolution 2.10&Aring;
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<StructureSection load='1od5' size='340' side='right'caption='[[1od5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Chain+B'>AC1</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
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<table><tr><td colspan='2'>[[1od5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OD5 FirstGlance]. <br>
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|ACTIVITY=
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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]] 2.1&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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|DOMAIN=
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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=1od5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1od5 OCA], [https://pdbe.org/1od5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1od5 RCSB], [https://www.ebi.ac.uk/pdbsum/1od5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1od5 ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1od5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1od5 OCA], [http://www.ebi.ac.uk/pdbsum/1od5 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1od5 RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/GLYG5_SOYBN GLYG5_SOYBN] Glycinin is the major seed storage protein of soybean (PubMed:2485233). Glycinin basic peptides (GBPs), and, to a lower extent, glycinin exhibit antibacterial activity against Gram-negative and Gram-positive bacteria (e.g. L.monocytogenes, B.subtilis, E.coli and S.enteritidis) by forming pores and aggregating in transmembranes, leading to membrane permeability and, eventually, cell death (PubMed:22236762, PubMed:28590128, Ref.15).<ref>PMID:22236762</ref> <ref>PMID:2485233</ref> <ref>PMID:28590128</ref> <ref>PMID:29037738</ref>
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== Evolutionary Conservation ==
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'''CRYSTAL STRUCTURE OF GLYCININ A3B4 SUBUNIT HOMOHEXAMER'''
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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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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/od/1od5_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=1od5 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 ==
Most plant seeds contain 11S globulins as major storage proteins for their nutrition. Soybean glycinin belongs to the 11S globulin family and consists of five kinds of subunits. We determined the crystal structure of a homohexamer of the glycinin A3B4 subunit at 2.1-A resolution. The crystal structure shows that the hexamer has 32-point group symmetry formed by face-to-face stacking of two trimers. The interface buries the highly conserved interchain disulfide. Based on the structure, we propose that an ingenious face-to-face mechanism controls the hexamer formation of the 11S globulin by movement of a mobile disordered region to the side of the trimer after posttranslational processing. Electrostatic analysis of the faces suggests that the interchain disulfide-containing face has high positive potential at acidic pH, which induces dissociation of the hexamer into trimers that may be susceptible to proteinases after seed imbibition. This dissociation might result in the degradation and mobilization of 11S globulins as storage proteins in embryos during germination and seedling growth.
Most plant seeds contain 11S globulins as major storage proteins for their nutrition. Soybean glycinin belongs to the 11S globulin family and consists of five kinds of subunits. We determined the crystal structure of a homohexamer of the glycinin A3B4 subunit at 2.1-A resolution. The crystal structure shows that the hexamer has 32-point group symmetry formed by face-to-face stacking of two trimers. The interface buries the highly conserved interchain disulfide. Based on the structure, we propose that an ingenious face-to-face mechanism controls the hexamer formation of the 11S globulin by movement of a mobile disordered region to the side of the trimer after posttranslational processing. Electrostatic analysis of the faces suggests that the interchain disulfide-containing face has high positive potential at acidic pH, which induces dissociation of the hexamer into trimers that may be susceptible to proteinases after seed imbibition. This dissociation might result in the degradation and mobilization of 11S globulins as storage proteins in embryos during germination and seedling growth.
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==About this Structure==
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Crystal structure of soybean 11S globulin: glycinin A3B4 homohexamer.,Adachi M, Kanamori J, Masuda T, Yagasaki K, Kitamura K, Mikami B, Utsumi S Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7395-400. Epub 2003 May 27. PMID:12771376<ref>PMID:12771376</ref>
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1OD5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD5 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of soybean 11S globulin: glycinin A3B4 homohexamer., Adachi M, Kanamori J, Masuda T, Yagasaki K, Kitamura K, Mikami B, Utsumi S, Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7395-400. Epub 2003 May 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12771376 12771376]
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</div>
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<div class="pdbe-citations 1od5" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Glycine max]]
[[Category: Glycine max]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Adachi, M.]]
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[[Category: Adachi M]]
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[[Category: Kanamori, J.]]
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[[Category: Kanamori J]]
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[[Category: Kitamura, K.]]
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[[Category: Kitamura K]]
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[[Category: Masuda, T.]]
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[[Category: Masuda T]]
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[[Category: Mikami, B.]]
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[[Category: Mikami B]]
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[[Category: Utsumi, S.]]
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[[Category: Utsumi S]]
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[[Category: Yagasaki, K.]]
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[[Category: Yagasaki K]]
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[[Category: 11s,seed storage protein]]
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[[Category: globulin]]
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[[Category: glycinin]]
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[[Category: soybean]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:43:29 2008''
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Current revision

Crystal structure of glycinin A3B4 subunit homohexamer

PDB ID 1od5

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