2d5f

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:54, 30 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2d5f.png|left|200px]]
 
-
<!--
+
==Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly==
-
The line below this paragraph, containing "STRUCTURE_2d5f", creates the "Structure Box" on the page.
+
<StructureSection load='2d5f' size='340' side='right'caption='[[2d5f]], [[Resolution|resolution]] 1.90&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'>[[2d5f]] 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=2D5F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D5F 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]] 1.9&#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=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-
{{STRUCTURE_2d5f| PDB=2d5f | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5f OCA], [https://pdbe.org/2d5f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d5f RCSB], [https://www.ebi.ac.uk/pdbsum/2d5f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d5f 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/d5/2d5f_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=2d5f ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structures of two pro-11S globulins namely: rapeseed procruciferin and pea prolegumin are presented here. We have extensively compared them with the other known structures of plant seed 11S and 7S globulins. In general, the disordered regions in the crystal structures among the 11S globulins correspond to their five variable regions. Variable region III of procruciferin is relatively short and is in a loop conformation. This region is highly disordered in other pro-11S globulin crystals. Local helical and strand variations also occur across the group despite general structure conservation. We showed how these variations may alter specific physicochemical, functional and physiological properties. Aliphatic hydrophobic residues on the molecular surface correlate well with Tm values of the globulins. We also considered other structural features that were reported to influence thermal stability but no definite conclusion was drawn since each factor has additive or subtractive effect. Comparison between proA3B4 and mature A3B4 revealed an increase in r.m.s.d. values near variable regions II and IV. Both regions are on the IE face. Secondary structure based alignment of 11S and 7S globulins revealed 16 identical residues. Based on proA3B4 sequence, Pro60, Gly128, Phe163, Phe208, Leu213, Leu227, Ile237, Pro382, Val404, Pro425 and Val 466 are involved in trimer formation and stabilization. Gly28, Gly74, Asp135, Gly349 and Gly397 are involved in correct globular folding.
-
===Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly===
+
Conservation and divergence on plant seed 11S globulins based on crystal structures.,Tandang-Silvas MR, Fukuda T, Fukuda C, Prak K, Cabanos C, Kimura A, Itoh T, Mikami B, Utsumi S, Maruyama N Biochim Biophys Acta. 2010 Jul;1804(7):1432-42. Epub 2010 Mar 6. PMID:20215054<ref>PMID:20215054</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_20215054}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2d5f" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 20215054 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20215054}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2D5F is a 2 chains structure with 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=2D5F OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:20215054</ref><references group="xtra"/>
+
[[Category: Glycine max]]
[[Category: Glycine max]]
-
[[Category: Adachi, M.]]
+
[[Category: Large Structures]]
-
[[Category: Itoh, T.]]
+
[[Category: Adachi M]]
-
[[Category: Masuda, T.]]
+
[[Category: Itoh T]]
-
[[Category: Mikami, B.]]
+
[[Category: Masuda T]]
-
[[Category: Utsumi, S.]]
+
[[Category: Mikami B]]
-
[[Category: 11]]
+
[[Category: Utsumi S]]
-
[[Category: Globulin]]
+
-
[[Category: Glycinin]]
+
-
[[Category: Plant protein]]
+
-
[[Category: Seed storage protein]]
+
-
[[Category: Soybean]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 21 09:10:10 2010''
+

Current revision

Crystal Structure of Recombinant Soybean Proglycinin A3B4 subunit, its Comparison with Mature Glycinin A3B4 subunit, Responsible for Hexamer Assembly

PDB ID 2d5f

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/2d5f"
Personal tools