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2buk

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SATELLITE TOBACCO NECROSIS VIRUS

Structural highlights

2buk is a 1 chain structure with sequence from Unidentified tobacco necrosis virus. This structure supersedes the now removed PDB entry 2stv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.45Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_STNV1 Self-assembles to form an icosahedral capsid of 17 nm in diameter.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The structure of the protein subunit of satellite tobacco necrosis virus has been solved at 3.7 A resolution. We have now crystallographically refined the original model and extended the resolution ot 2.5 A in order to get a model accurate enough to explain the details of the subunit interactions. The refinement was done with a novel method utilizing the icosahedral symmetry of the virus particle. The final model shows a complicated network of interactions, involving salt linkages, hydrogen bonds and hydrophobic contacts. In addition, we have located three different metal ion sites in the protein shell, linking the protein subunits together. These sites are probably occupied by calcium ions. One site is found in a general position near the icosahedral 3-fold axis of the virus. The ligands form an octahedral arrangement, with two main chain carbonyl oxygens (0-61 and 0-64), one carboxylate oxygen (OD1 from Asp194) of the same subunit and a second carboxylate oxygen (OE1 of Glu25) from a 3-fold related subunit. Two water molecules complete the octahedral arrangement. A second site is on the icosahedral 3-fold axis and is liganded by the carboxylate oxygens of the 3-fold related Asp55 residues. The third metal ion site is found on the 5-fold axis, liganded by the five carbonyl oxygens of Thr138 and two water molecules. We are unable to locate the first 11 N-terminal amino acid residues, which point into the virus interior. No interpretable density for RNA has been found, indicating that the nucleic acid of the virus does not have a unique orientation in the crystal.

Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution.,Jones TA, Liljas L J Mol Biol. 1984 Aug 25;177(4):735-67. PMID:6481804^[4]

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

References

↑ Lane SW, Dennis CA, Lane CL, Trinh CH, Rizkallah PJ, Stockley PG, Phillips SE. Construction and Crystal Structure of Recombinant STNV Capsids. J Mol Biol. 2011 Oct 14;413(1):41-50. Epub 2011 Aug 3. PMID:21839089 doi:10.1016/j.jmb.2011.07.062
↑ Ford RJ, Barker AM, Bakker SE, Coutts RH, Ranson NA, Phillips SE, Pearson AR, Stockley PG. Sequence-Specific, RNA-Protein Interactions Overcome Electrostatic Barriers Preventing Assembly of Satellite Tobacco Necrosis Virus Coat Protein. J Mol Biol. 2013 Jan 11. pii: S0022-2836(13)00007-7. doi:, 10.1016/j.jmb.2013.01.004. PMID:23318955 doi:http://dx.doi.org/10.1016/j.jmb.2013.01.004
↑ Jones TA, Liljas L. Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution. J Mol Biol. 1984 Aug 25;177(4):735-67. PMID:6481804
↑ Jones TA, Liljas L. Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution. J Mol Biol. 1984 Aug 25;177(4):735-67. PMID:6481804

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2buk"

Categories: Large Structures | Unidentified tobacco necrosis virus | Jones TA | Liljas L

@@ Line 1: / Line 1: @@
 ==SATELLITE TOBACCO NECROSIS VIRUS==
-<StructureSection load='2buk' size='340' side='right' caption='[[2buk]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+<StructureSection load='2buk' size='340' side='right'caption='[[2buk]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2buk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Unidentified_tobacco_necrosis_virus Unidentified tobacco necrosis virus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2stv 2stv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BUK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2buk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Unidentified_tobacco_necrosis_virus Unidentified tobacco necrosis virus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2stv 2stv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BUK FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</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=2buk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2buk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2buk RCSB], [http://www.ebi.ac.uk/pdbsum/2buk PDBsum]</span></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>
-<table>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2buk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2buk OCA], [https://pdbe.org/2buk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2buk RCSB], [https://www.ebi.ac.uk/pdbsum/2buk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2buk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSD_STNV1 CAPSD_STNV1] Self-assembles to form an icosahedral capsid of 17 nm in diameter.<ref>PMID:21839089</ref> <ref>PMID:23318955</ref> <ref>PMID:6481804</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 14: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2buk" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Virus coat protein|Virus coat protein]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Unidentified tobacco necrosis virus]]
-[[Category: Jones, T A.]]
+[[Category: Jones TA]]
-[[Category: Liljas, L.]]
+[[Category: Liljas L]]
-[[Category: Capsid]]
-[[Category: Icosahedral virus]]
-[[Category: Tobacco necrosis satellite virus]]
-[[Category: Virus]]
-[[Category: Virus/viral protein]]

2buk

From Proteopedia

Current revision

SATELLITE TOBACCO NECROSIS VIRUS

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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