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| ==The Structure of Major Capsid protein of a large, lipid containing, DNA virus==
| | #REDIRECT [[5tip]] This PDB entry is obsolete and replaced by 5tip |
| <StructureSection load='1m3y' size='340' side='right' caption='[[1m3y]], [[Resolution|resolution]] 2.00Å' scene=''>
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| == Structural highlights ==
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| <table><tr><td colspan='2'>[[1m3y]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlorella_pbcv-1_virus Chlorella pbcv-1 virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M3Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M3Y FirstGlance]. <br>
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| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
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| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j5q|1j5q]], [[1m4x|1m4x]]</td></tr>
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| <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=1m3y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3y OCA], [http://pdbe.org/1m3y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m3y RCSB], [http://www.ebi.ac.uk/pdbsum/1m3y PDBsum]</span></td></tr>
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| </table>
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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/m3/1m3y_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=1m3y 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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| Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.
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| The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus.,Nandhagopal N, Simpson AA, Gurnon JR, Yan X, Baker TS, Graves MV, Van Etten JL, Rossmann MG Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14758-63. Epub 2002 Oct 31. PMID:12411581<ref>PMID:12411581</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 1m3y" style="background-color:#fffaf0;"></div>
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| ==See Also==
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| *[[Temperature value vs. resolution|Temperature value vs. resolution]]
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| *[[Virus coat protein|Virus coat protein]]
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| == References ==
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| <references/>
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| __TOC__
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| </StructureSection>
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| [[Category: Chlorella pbcv-1 virus]]
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| [[Category: Baker, T S]]
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| [[Category: Etten, J L.Van]]
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| [[Category: Graves, M V]]
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| [[Category: Gurnon, J R]]
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| [[Category: Nandhagopal, N]]
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| [[Category: Rossmann, M G]]
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| [[Category: Simpson, A A]]
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| [[Category: Yan, X]]
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| [[Category: Chlorella virus]]
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| [[Category: Glycoprotein]]
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| [[Category: Jelly roll motif]]
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| [[Category: Major capsit protein vp54]]
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| [[Category: Pbcv-1]]
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| [[Category: Viral protein]]
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