1od5

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:32, 23 October 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1od5.png|left|200px]]
 
-
<!--
+
==Crystal structure of glycinin A3B4 subunit homohexamer==
-
The line below this paragraph, containing "STRUCTURE_1od5", creates the "Structure Box" on the page.
+
<StructureSection load='1od5' size='340' side='right'caption='[[1od5]], [[Resolution|resolution]] 2.10&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'>[[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>
-
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]] 2.1&#8491;</td></tr>
-
-->
+
<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>
-
{{STRUCTURE_1od5| PDB=1od5 | SCENE= }}
+
<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>
 +
</table>
 +
== Function ==
 +
[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>
 +
== 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/od/1od5_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=1od5 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
===CRYSTAL STRUCTURE OF GLYCININ A3B4 SUBUNIT HOMOHEXAMER===
+
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>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_12771376}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 1od5" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 12771376 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_12771376}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
1OD5 is a 2 chains structure of sequences 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].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:12771376</ref><references group="xtra"/>
+
[[Category: Glycine max]]
[[Category: Glycine max]]
-
[[Category: Adachi, M.]]
+
[[Category: Large Structures]]
-
[[Category: Kanamori, J.]]
+
[[Category: Adachi M]]
-
[[Category: Kitamura, K.]]
+
[[Category: Kanamori J]]
-
[[Category: Masuda, T.]]
+
[[Category: Kitamura K]]
-
[[Category: Mikami, B.]]
+
[[Category: Masuda T]]
-
[[Category: Utsumi, S.]]
+
[[Category: Mikami B]]
-
[[Category: Yagasaki, K.]]
+
[[Category: Utsumi S]]
-
[[Category: 11s,seed storage protein]]
+
[[Category: Yagasaki K]]
-
[[Category: Globulin]]
+
-
[[Category: Glycinin]]
+
-
[[Category: Soybean]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:24:47 2009''
+

Current revision

Crystal structure of glycinin A3B4 subunit homohexamer

PDB ID 1od5

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1od5"
Personal tools