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1rmv

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Revision as of 07:18, 22 September 2021

RIBGRASS MOSAIC VIRUS, FIBER DIFFRACTION

Structural highlights

1rmv is a 2 chain structure with sequence from Ribgrass mosaic virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

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

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1rmv"

@@ Line 3: / Line 3: @@
 <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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMV FirstGlance]. <br>
+<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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmv OCA], [http://pdbe.org/1rmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rmv RCSB], [http://www.ebi.ac.uk/pdbsum/1rmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmv ProSAT]</span></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 ==
-[[http://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.
+[[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]]
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[Virus coat protein|Virus coat protein]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 == References ==
 <references/>

1rmv

From Proteopedia

Revision as of 07:18, 22 September 2021

RIBGRASS MOSAIC VIRUS, FIBER DIFFRACTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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