View source for 1rmv


==RIBGRASS MOSAIC VIRUS, FIBER DIFFRACTION==
<StructureSection load='1rmv' size='340' side='right'caption='[[1rmv]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1rmv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ribgrass_mosaic_virus Ribgrass mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMV FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Fiber diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></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=1rmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmv OCA], [https://pdbe.org/1rmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmv RCSB], [https://www.ebi.ac.uk/pdbsum/1rmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CAPSD_RMVHR CAPSD_RMVHR] Capsid protein self-assembles to form rod-shaped virions about 18 nm in diameter with a central canal enclosing the viral genomic RNA.
== 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/rm/1rmv_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=1rmv ConSurf].
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== Publication Abstract from PubMed ==
The molecular dynamics (MD) method has been adapted for refinement of the structures of helical macromolecular aggregates aginst X-ray fiber diffraction data. To test the effectiveness of the method, refinements of the tobacco mosaic virus structure were carried out against a set of simulated fiber diffraction intensities using the MD method as well as the conventional restrained least-squares (RLS) method. The MD refinement converged to a very low R factor and produced a structure with generally satisfactory sterochemistry, while the RLS refinemnt was trapped at a local energy minimum with a larger R factor. Results suggest that the effective experimental radius of convergence of the MD method is significantly greater than that of the RLS method. Even when the initial structure is too far from the true structure to allow direct refinement, the MD method is able to find local minima that resemble the true structure sufficiently to allow improved phasing and thus lead to interpretable difference maps for model rebuilding.

Molecular dynamics in refinement against fiber diffraction data.,Wang H, Stubbs G Acta Crystallogr A. 1993 May 1;49(3):504-13. PMID:8129880<ref>PMID:8129880</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1rmv" style="background-color:#fffaf0;"></div>

==See Also==
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Ribgrass mosaic virus]]
[[Category: Stubbs G]]
[[Category: Wang H]]