4nia - Revision history

OCA at 16:57, 20 September 2023

OCA — Wed, 20 Sep 2023 16:57:43 GMT

←Older revision		Revision as of 16:57, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nia]] is a 60 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=4NIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nia]] is a 60 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=4NIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NIA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.82Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [https://pdbe.org/4nia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [https://www.ebi.ac.uk/pdbsum/4nia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nia 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=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [https://pdbe.org/4nia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [https://www.ebi.ac.uk/pdbsum/4nia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nia ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:29, 11 January 2023

OCA — Wed, 11 Jan 2023 08:29:46 GMT

←Older revision		Revision as of 08:29, 11 January 2023
Line 3:		Line 3:
	<StructureSection load='4nia' size='340' side='right'caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='4nia' size='340' side='right'caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [~~http://en.wikipedia.org/wiki/Satellite_tobacco_mosaic_virus Satellite tobacco mosaic virus] and [http~~://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=4NIA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nia]] is a 60 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=4NIA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NIA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]~~</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=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [https://pdbe.org/4nia PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [https://www.ebi.ac.uk/pdbsum/4nia PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nia ProSAT]</span></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=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [~~http~~://pdbe.org/4nia PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nia PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4nia ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/COAT_STMV COAT_STMV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:
	==See Also==		==See Also==
	*[[Tobacco Mosaic Virus\|Tobacco Mosaic Virus]]		*[[Tobacco Mosaic Virus\|Tobacco Mosaic Virus]]
-	*[[Virus coat ~~protein~~\|Virus coat ~~protein~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 28:
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Satellite tobacco mosaic virus]]		[[Category: Satellite tobacco mosaic virus]]
-	[[Category: Day~~, J S~~]]	+	[[Category: Day JS]]
-	[[Category: Larson~~, S B~~]]	+	[[Category: Larson SB]]
-	[[Category: McPherson, A]]	+	[[Category: McPherson A]]
-	~~[[Category: Double-helix rna]]~~	+
-	~~[[Category: Icosahedral virus]]~~	+
-	~~[[Category: Protein-rna complex]]~~	+
-	~~[[Category: Swiss jelly-roll beta barrel]]~~	+
-	~~[[Category: Virus-rna complex~~]]	+

OCA at 05:24, 13 February 2020

OCA — Thu, 13 Feb 2020 05:24:46 GMT

←Older revision		Revision as of 05:24, 13 February 2020
Line 1:		Line 1:

	==Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints==		==Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints==
-	<StructureSection load='4nia' size='340' side='right' caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>	+	<StructureSection load='4nia' size='340' side='right'caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Satellite_tobacco_mosaic_virus Satellite tobacco mosaic virus] and [http://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=4NIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Satellite_tobacco_mosaic_virus Satellite tobacco mosaic virus] and [http://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=4NIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIA FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4nia" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4nia" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Tobacco Mosaic Virus\|Tobacco Mosaic Virus]]
		+	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Satellite tobacco mosaic virus]]		[[Category: Satellite tobacco mosaic virus]]
	[[Category: Day, J S]]		[[Category: Day, J S]]

OCA at 08:14, 22 November 2017

OCA — Wed, 22 Nov 2017 08:14:28 GMT

←Older revision		Revision as of 08:14, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4nia' size='340' side='right' caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='4nia' size='340' side='right' caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Tobacco_necrosis_satellite_virus Tobacco necrosis satellite~~ virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Satellite_tobacco_mosaic_virus Satellite tobacco mosaic virus] and [http://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=4NIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Tobacco necrosis satellite~~ virus]]	+	[[Category: Satellite tobacco mosaic virus]]
	[[Category: Day, J S]]		[[Category: Day, J S]]
	[[Category: Larson, S B]]		[[Category: Larson, S B]]

OCA at 20:13, 11 August 2016

OCA — Thu, 11 Aug 2016 20:13:11 GMT

←Older revision		Revision as of 20:13, 11 August 2016
Line 1:		Line 1:
		+
	==Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints==		==Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints==
	<StructureSection load='4nia' size='340' side='right' caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='4nia' size='340' side='right' caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]</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=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [http://www.ebi.ac.uk/pdbsum/4nia PDBsum]</span></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=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [http://pdbe.org/4nia PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [http://www.ebi.ac.uk/pdbsum/4nia PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nia ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4nia" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:43, 20 January 2015

OCA — Tue, 20 Jan 2015 10:43:54 GMT

←Older revision		Revision as of 10:43, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Tobacco_necrosis_satellite_virus Tobacco necrosis satellite virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Tobacco_necrosis_satellite_virus Tobacco necrosis satellite virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [http://www.ebi.ac.uk/pdbsum/4nia PDBsum]</span></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=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [http://www.ebi.ac.uk/pdbsum/4nia PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Tobacco necrosis satellite virus]]		[[Category: Tobacco necrosis satellite virus]]
-	[[Category: Day, J S.]]	+	[[Category: Day, J S]]
-	[[Category: Larson, S B.]]	+	[[Category: Larson, S B]]
-	[[Category: McPherson, A.]]	+	[[Category: McPherson, A]]
	[[Category: Double-helix rna]]		[[Category: Double-helix rna]]
	[[Category: Icosahedral virus]]		[[Category: Icosahedral virus]]

OCA at 22:11, 1 October 2014

OCA — Wed, 01 Oct 2014 22:11:48 GMT

←Older revision		Revision as of 22:11, 1 October 2014
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~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.	+	Satellite tobacco mosaic virus (STMV) is among the smallest viruses, having 60 identical subunits arranged with T = 1 icosahedral symmetry. Its crystal structure was solved at 290 K and was refined using, in part, crystals grown in microgravity. Electron-density maps revealed nearly 57% of the genomic ssRNA. Using six flash-cooled crystals, diffraction data were recorded to 1.4 A resolution and independent refinements of the STMV model were carried out versus the previous 1.8 A resolution data representing merged data from 21 crystals (271 689 unique reflections), data consisting of corresponding reflections to 1.8 A resolution from the cooled crystals and 1.4 A resolution data from the cooled crystals comprised of 570 721 unique reflections. Models were independently refined with full NCS constraints using the program CNS and in restrained mode using the programs CNS, REFMAC5 and SHELX-97, with the latter two procedures including anisotropic temperature factors. Significant additional structural detail emerged from the analyses, including a unique cation and anion arrangement on fivefold axes and a precise assessment of icosahedral symmetry exactness in the crystal lattice. STMV represents the highest resolution native virus structure currently known by a substantial margin, and it permits the evaluation of a precise atomic model of a spherical virus at near-atomic resolution for the first time.

-	~~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:~~9514737~~<ref>PMID:~~9514737~~</ref>	+	Satellite tobacco mosaic virus refined to 1.4 A resolution.,Larson SB, Day JS, McPherson A Acta Crystallogr D Biol Crystallogr. 2014 Sep 1;70(Pt 9):2316-30. doi:, 10.1107/S1399004714013789. Epub 2014 Aug 29. PMID:25195746<ref>PMID:25195746</ref>

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

OCA at 10:01, 10 September 2014

OCA — Wed, 10 Sep 2014 10:01:50 GMT

←Older revision		Revision as of 10:01, 10 September 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints==
		+	<StructureSection load='4nia' size='340' side='right' caption='[[4nia]], [[Resolution\|resolution]] 1.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4nia]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Tobacco_necrosis_satellite_virus Tobacco necrosis satellite virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NIA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NIA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a34\|1a34]], [[4oq8\|4oq8]], [[4oq9\|4oq9]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4nia FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nia OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nia RCSB], [http://www.ebi.ac.uk/pdbsum/4nia PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.

-	~~The entry 4nia is ON HOLD until Paper Publication~~	+	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:9514737<ref>PMID:9514737</ref>

-	~~Authors: Larson~~, S.B., Day, J.S., McPherson, A.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Satellite Tobacco Mosaic~~ Virus ~~Refined at room temperature to 1.8 A Resolution using NCS Restraints~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tobacco necrosis satellite virus]]
		+	[[Category: Day, J S.]]
		+	[[Category: Larson, S B.]]
		+	[[Category: McPherson, A.]]
		+	[[Category: Double-helix rna]]
		+	[[Category: Icosahedral virus]]
		+	[[Category: Protein-rna complex]]
		+	[[Category: Swiss jelly-roll beta barrel]]
		+	[[Category: Virus-rna complex]]

OCA at 12:06, 12 March 2014

OCA — Wed, 12 Mar 2014 12:06:39 GMT

←Older revision		Revision as of 12:06, 12 March 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nia is ON HOLD	+	The entry 4nia is ON HOLD until Paper Publication

	Authors: Larson, S.B., Day, J.S., McPherson, A.		Authors: Larson, S.B., Day, J.S., McPherson, A.

-	Description: Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 AA Resolution using NCS Restraints	+	Description: Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints

OCA at 13:04, 11 December 2013

OCA — Wed, 11 Dec 2013 13:04:02 GMT

←Older revision		Revision as of 13:04, 11 December 2013
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	The entry 4nia is ON HOLD		The entry 4nia is ON HOLD

-	Authors: Larson, S. B., Day, J. S., McPherson, A.	+	Authors: Larson, S.B., Day, J.S., McPherson, A.

	Description: Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 AA Resolution using NCS Restraints		Description: Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 AA Resolution using NCS Restraints