1f2n: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1f2n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rice_yellow_mottle_virus Rice yellow mottle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F2N FirstGlance]. <br>
<table><tr><td colspan='2'>[[1f2n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rice_yellow_mottle_virus Rice yellow mottle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F2N FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1f2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f2n OCA], [https://pdbe.org/1f2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f2n RCSB], [https://www.ebi.ac.uk/pdbsum/1f2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f2n 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=1f2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f2n OCA], [https://pdbe.org/1f2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f2n RCSB], [https://www.ebi.ac.uk/pdbsum/1f2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f2n ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q86527_9VIRU Q86527_9VIRU]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1f2n ConSurf].
</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=1f2n ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Rice yellow mottle virus (RYMV) is a major pathogen that dramatically reduces rice production in many African countries. RYMV belongs to the genus sobemovirus, one group of plant viruses with icosahedral capsids and single-stranded, positive-sense RNA genomes. RESULTS: The structure of RYMV was determined and refined to 2.8 A resolution by X-ray crystallography. The capsid contains 180 copies of the coat protein subunit arranged with T = 3 icosahedral symmetry. Each subunit adopts a jelly-roll beta sandwich fold. The RYMV capsid structure is similar to those of other sobemoviruses. When compared with these viruses, however, the betaA arm of the RYMV C subunit, which is a molecular switch that regulates quasi-equivalent subunit interactions, is swapped with the 2-fold-related betaA arm to a similar, noncovalent bonding environment. This exchange of identical structural elements across a symmetry axis is categorized as 3D domain swapping and produces long-range interactions throughout the icosahedral surface lattice. Biochemical analysis supports the notion that 3D domain swapping increases the stability of RYMV. CONCLUSIONS: The quasi-equivalent interactions between the RYMV proteins are regulated by the N-terminal ordered residues of the betaA arm, which functions as a molecular switch. Comparative analysis suggests that this molecular switch can also modulate the stability of the viral capsids.
3D domain swapping modulates the stability of members of an icosahedral virus group.,Qu C, Liljas L, Opalka N, Brugidou C, Yeager M, Beachy RN, Fauquet CM, Johnson JE, Lin T Structure. 2000 Oct 15;8(10):1095-103. PMID:11080631<ref>PMID:11080631</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1f2n" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Rice yellow mottle virus]]
[[Category: Rice yellow mottle virus]]
[[Category: Beachy, R N]]
[[Category: Beachy RN]]
[[Category: Brugidou, C]]
[[Category: Brugidou C]]
[[Category: Fauquet, C M]]
[[Category: Fauquet CM]]
[[Category: Johnson, J E]]
[[Category: Johnson JE]]
[[Category: Liljas, L]]
[[Category: Liljas L]]
[[Category: Lin, T]]
[[Category: Lin T]]
[[Category: Opalka, N]]
[[Category: Opalka N]]
[[Category: Qu, C]]
[[Category: Qu C]]
[[Category: Yeager, M]]
[[Category: Yeager M]]
[[Category: Beta-annulus]]
[[Category: Capsid protein]]
[[Category: Coat protein]]
[[Category: Domain swapping]]
[[Category: Icosahedral virus]]
[[Category: Plant virus]]
[[Category: Virus]]

Latest revision as of 07:09, 7 February 2024

RICE YELLOW MOTTLE VIRUS

1f2n, resolution 2.80Å

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