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1a34

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(New page: 200px<br /><applet load="1a34" size="450" color="white" frame="true" align="right" spinBox="true" caption="1a34, resolution 1.810&Aring;" /> '''SATELLITE TOBACCO M...)
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[[Image:1a34.gif|left|200px]]<br /><applet load="1a34" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1a34, resolution 1.810&Aring;" />
 
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'''SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX'''<br />
 
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==Overview==
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==SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX==
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The molecular structure of satellite tobacco mosaic virus (STMV) has been, refined to 1.8 A resolution using X-ray diffraction data collected from, crystals grown in microgravity. The final R value was 0.179 and Rfree was, 0.184 for 219,086 independent reflections. The final model of the, asymmetric unit contained amino acid residues 13 to 159 of a coat protein, monomer, 21 nucleotides, a sulfate ion, and 168 water molecules. The, nucleotides were visualized as 30 helical segments of nine base-pairs with, an additional base stacked at each 3' end, plus a "free" nucleotide, not, belonging to the helical segments, but firmly bound by the protein., Sulfate ions are located exactly on 5-fold axes and each is coordinated by, ten asparagine side-chains. Of the 10,080 structural waters, 168 per, asymmetric unit, about 20% serve to bridge the macromolecular components, at protein-protein and protein-nucleic acid interfaces.Binding of RNA to, the protein involves some salt linkages, particularly to the phosphate of, the free nucleotide, but the major contribution is from an intricate, network of hydrogen bonds. There are numerous water molecules in the, RNA-protein interface, many serving as intermediate hydrogen bond bridges., The sugar-phosphate backbone contributes most of the donors and acceptors, for the RNA. The helical RNA conformation is nearest that of A form DNA., The central region of a helical segment is most extensively involved in, contacts with protein, and exhibits low thermal parameters which increase, dramatically toward the ends. The visible RNA represents approximately 59%, of the total nucleic acid in the virion and is derived from the, single-stranded genome, which has folded upon itself to form helical, segments. Linking of the helices and the free nucleotides in a contiguous, and efficient manner severely restricts the disposition of the remaining, unseen nucleic acid. Using the remaining nucleotides it is possible to, fold the RNA according to motifs that provide a periodic distribution of, RNA structural elements compatible with the icosahedrally symmetrical, arrangement seen in the crystallographic structure. The intimate, relationship between protein and nucleic acid in STMV suggests an assembly, pathway based on the cooperative and coordinated co-condensation of RNA, with capsid protein dimers.
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<StructureSection load='1a34' size='340' side='right'caption='[[1a34]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1a34]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Satellite_tobacco_mosaic_virus Satellite tobacco mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A34 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.81&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1a34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a34 OCA], [https://pdbe.org/1a34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a34 RCSB], [https://www.ebi.ac.uk/pdbsum/1a34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a34 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/COAT_STMV COAT_STMV]
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==About this Structure==
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==See Also==
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1A34 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Tobacco_necrosis_satellite_virus Tobacco necrosis satellite virus] with SO4 and U as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1A34 OCA].
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*[[Tobacco Mosaic Virus|Tobacco Mosaic Virus]]
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__TOC__
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==Reference==
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</StructureSection>
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Refined structure of satellite tobacco mosaic virus at 1.8 A resolution., Larson SB, Day J, Greenwood A, McPherson A, J Mol Biol. 1998 Mar 20;277(1):37-59. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9514737 9514737]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Satellite tobacco mosaic virus]]
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[[Category: Tobacco necrosis satellite virus]]
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[[Category: Day J]]
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[[Category: Day, J.]]
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[[Category: Greenwood AJ]]
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[[Category: Greenwood, A.J.]]
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[[Category: Larson SB]]
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[[Category: Larson, S.B.]]
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[[Category: McPherson A]]
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[[Category: McPherson, A.]]
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[[Category: SO4]]
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[[Category: U]]
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[[Category: icosahedral virus]]
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[[Category: macromolecular interactions]]
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[[Category: rna]]
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[[Category: satellite tobacco mosaic virus]]
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[[Category: virus assembly]]
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[[Category: water structure]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:34:53 2007''
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Current revision

SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX

PDB ID 1a34

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