1vd0: Difference between revisions

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[[Image:1vd0.png|left|200px]]


<!--
==Capsid stabilizing protein GPD, NMR, 20 Structures==
The line below this paragraph, containing "STRUCTURE_1vd0", creates the "Structure Box" on the page.
<StructureSection load='1vd0' size='340' side='right'caption='[[1vd0]]' 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'>[[1vd0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VD0 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">Solution NMR</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=1vd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vd0 OCA], [https://pdbe.org/1vd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vd0 RCSB], [https://www.ebi.ac.uk/pdbsum/1vd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vd0 ProSAT], [https://www.topsan.org/Proteins/RSGI/1vd0 TOPSAN]</span></td></tr>
{{STRUCTURE_1vd0|  PDB=1vd0  |  SCENE=  }}
</table>
 
== Function ==
===Capsid stabilizing protein GPD, NMR, 20 Structures===
[https://www.uniprot.org/uniprot/DECO_LAMBD DECO_LAMBD] Stabilizes the expansion of the capsid head shell after genome packaging. The packaging of viral genome in the procapsid triggers a dramatic reconfiguration of the capsid shell, expanding from roughly 50nm to 60nm while the capsid thickness decreases. 415 capsid decoration protein molecules cooperatively bind the expanded capsid, thereby stabilizing the mature capsid shell.<ref>PMID:18786402</ref> <ref>PMID:21821043</ref> <ref>PMID:8411174</ref>
 
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
==About this Structure==
Check<jmol>
[[1vd0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_lambda Enterobacteria phage lambda]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VD0 OCA].  
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vd/1vd0_consurf.spt"</scriptWhenChecked>
==Reference==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<ref group="xtra">PMID:15929002</ref><ref group="xtra">PMID:14739644</ref><references group="xtra"/>
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Enterobacteria phage lambda]]
  </jmolCheckbox>
[[Category: Forrer, P.]]
</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=1vd0 ConSurf].
[[Category: Guntert, P.]]
<div style="clear:both"></div>
[[Category: Iwai, H.]]
== References ==
[[Category: Pluckthun, A.]]
<references/>
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
__TOC__
[[Category: Capsid protein]]
</StructureSection>
[[Category: National project on protein structural and functional analyse]]
[[Category: Escherichia virus Lambda]]
[[Category: Nppsfa]]
[[Category: Large Structures]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Forrer P]]
[[Category: Rsgi]]
[[Category: Guntert P]]
[[Category: Scottish structural proteomics facility]]
[[Category: Iwai H]]
[[Category: Sspf]]
[[Category: Pluckthun A]]
[[Category: Structural genomic]]
[[Category: Virus/viral protein]]

Latest revision as of 03:01, 28 December 2023

Capsid stabilizing protein GPD, NMR, 20 StructuresCapsid stabilizing protein GPD, NMR, 20 Structures

Structural highlights

1vd0 is a 1 chain structure with sequence from Escherichia virus Lambda. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

DECO_LAMBD Stabilizes the expansion of the capsid head shell after genome packaging. The packaging of viral genome in the procapsid triggers a dramatic reconfiguration of the capsid shell, expanding from roughly 50nm to 60nm while the capsid thickness decreases. 415 capsid decoration protein molecules cooperatively bind the expanded capsid, thereby stabilizing the mature capsid shell.[1] [2] [3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Lander GC, Evilevitch A, Jeembaeva M, Potter CS, Carragher B, Johnson JE. Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM. Structure. 2008 Sep 10;16(9):1399-406. doi: 10.1016/j.str.2008.05.016. PMID:18786402 doi:http://dx.doi.org/10.1016/j.str.2008.05.016
  2. ↑ Medina EM, Andrews BT, Nakatani E, Catalano CE. The bacteriophage lambda gpNu3 scaffolding protein is an intrinsically disordered and biologically functional procapsid assembly catalyst. J Mol Biol. 2011 Sep 30;412(4):723-36. doi: 10.1016/j.jmb.2011.07.045. Epub 2011 , Jul 29. PMID:21821043 doi:http://dx.doi.org/10.1016/j.jmb.2011.07.045
  3. ↑ Dokland T, Murialdo H. Structural transitions during maturation of bacteriophage lambda capsids. J Mol Biol. 1993 Oct 20;233(4):682-94. PMID:8411174 doi:http://dx.doi.org/10.1006/jmbi.1993.1545
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