1laj

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[[Image:1laj.gif|left|200px]]
 
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{{Structure
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==The Structure of Tomato Aspermy Virus by X-Ray Crystallography==
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|PDB= 1laj |SIZE=350|CAPTION= <scene name='initialview01'>1laj</scene>, resolution 3.4&Aring;
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<StructureSection load='1laj' size='340' side='right'caption='[[1laj]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
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<table><tr><td colspan='2'>[[1laj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Tomato_aspermy_virus Tomato aspermy virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LAJ FirstGlance]. <br>
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|ACTIVITY=
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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]] 3.4&#8491;</td></tr>
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|GENE=
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<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></td></tr>
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|DOMAIN=
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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=1laj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1laj OCA], [https://pdbe.org/1laj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1laj RCSB], [https://www.ebi.ac.uk/pdbsum/1laj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1laj ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1f15|1F15]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1laj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1laj OCA], [http://www.ebi.ac.uk/pdbsum/1laj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1laj RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/CAPSD_TAV CAPSD_TAV] Capsid protein. Probably binds RNA and plays a role in packaging (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/la/1laj_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1laj ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The three-dimensional structure of tomato aspermy virus (TAV) has been solved by X-ray crystallography and refined to an R factor of 0.218 for 3.4-40 A data (effective resolution of 4A). Molecular replacement, using cucumber mosaic virus (Smith et al., 2000), provided phases for the initial maps used for model building. The coat protein of the 280 A diameter virion has the canonical "Swiss roll" beta-barrel topology with a distinctive amino-terminal alpha-helix directed into the interior of the virus where it interacts with encapsidated RNA. The N-terminal helices are joined to the beta-barrels of protein subunits by extended polypeptides of six amino acids, which serve as flexible hinges allowing movement of the helices in response to local RNA distribution. Segments of three nucleotides of partially disordered RNA interact with the capsid, primarily through arginine residues, at interfaces between A and B subunits. Side chains of cys64 and cys106 form the first disulfide observed in a cucumovirus, including a unique cysteine, 106, in a region otherwise conserved. A positive ion, putatively modeled as a Mg(+)ion, lies on the quasi-threefold axis surrounded by three quasi-symmetric glutamate 175 side chains.
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'''The Structure of Tomato Aspermy Virus by X-Ray Crystallography'''
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The structure of tomato aspermy virus by X-ray crystallography.,Lucas RW, Larson SB, Canady MA, McPherson A J Struct Biol. 2002 Aug;139(2):90-102. PMID:12406691<ref>PMID:12406691</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1laj" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The three-dimensional structure of tomato aspermy virus (TAV) has been solved by X-ray crystallography and refined to an R factor of 0.218 for 3.4-40 A data (effective resolution of 4A). Molecular replacement, using cucumber mosaic virus (Smith et al., 2000), provided phases for the initial maps used for model building. The coat protein of the 280 A diameter virion has the canonical "Swiss roll" beta-barrel topology with a distinctive amino-terminal alpha-helix directed into the interior of the virus where it interacts with encapsidated RNA. The N-terminal helices are joined to the beta-barrels of protein subunits by extended polypeptides of six amino acids, which serve as flexible hinges allowing movement of the helices in response to local RNA distribution. Segments of three nucleotides of partially disordered RNA interact with the capsid, primarily through arginine residues, at interfaces between A and B subunits. Side chains of cys64 and cys106 form the first disulfide observed in a cucumovirus, including a unique cysteine, 106, in a region otherwise conserved. A positive ion, putatively modeled as a Mg(+)ion, lies on the quasi-threefold axis surrounded by three quasi-symmetric glutamate 175 side chains.
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*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1LAJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Tomato_aspermy_virus Tomato aspermy virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LAJ OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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The structure of tomato aspermy virus by X-ray crystallography., Lucas RW, Larson SB, Canady MA, McPherson A, J Struct Biol. 2002 Aug;139(2):90-102. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12406691 12406691]
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[[Category: Single protein]]
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[[Category: Tomato aspermy virus]]
[[Category: Tomato aspermy virus]]
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[[Category: Canady, M A.]]
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[[Category: Canady MA]]
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[[Category: Larson, S B.]]
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[[Category: Larson SB]]
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[[Category: Lucas, R W.]]
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[[Category: Lucas RW]]
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[[Category: McPherson, A.]]
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[[Category: McPherson A]]
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[[Category: anti-parallel beta sheet]]
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[[Category: disulphide bridge]]
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[[Category: icosahedral virus]]
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[[Category: jelly roll]]
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[[Category: protein-rna complex]]
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[[Category: t=3 icosahedral virus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:00:20 2008''
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Current revision

The Structure of Tomato Aspermy Virus by X-Ray Crystallography

PDB ID 1laj

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