1pgw: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==BEAN POD MOTTLE VIRUS (BPMV), TOP COMPONENT==
-<StructureSection load='1pgw' size='340' side='right' caption='[[1pgw]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='1pgw' size='340' side='right'caption='[[1pgw]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pgw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PGW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pgw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bean-pod_mottle_virus_(strain_Kentucky_G7) Bean-pod mottle virus (strain Kentucky G7)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PGW FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1bmv|1bmv]], [[1pgl|1pgl]], [[1ny7|1ny7]]</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]] 2.9&#8491;</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=1pgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgw OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pgw RCSB], [http://www.ebi.ac.uk/pdbsum/1pgw PDBsum]</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=1pgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pgw OCA], [https://pdbe.org/1pgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pgw RCSB], [https://www.ebi.ac.uk/pdbsum/1pgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pgw ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VGNM_BPMV VGNM_BPMV]] Movement protein: transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Acts by forming a tubular structure at the host plasmodesmata, enlarging it enough to allow free passage of virion capsids (By similarity).
+[https://www.uniprot.org/uniprot/POL2_BPMV POL2_BPMV] Movement protein: transports viral genome to neighboring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. Acts by forming a tubular structure at the host plasmodesmata, enlarging it enough to allow free passage of virion capsids (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/1pgw_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/1pgw_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1pgw ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Ordered nucleic acid in an icosahedral virus was first visualized in the X-ray structure of the Picorna-like plant virus, Bean pod mottle virus (BPMV). Virus particles containing the 3500 nucleotide segment of the BPMV bipartite RNA genome (middle component) had nearly 20% of the genome ordered. Here we report the refined structures of the middle component, bottom component (particles containing the 5800 nucleotide segment of the genome), and top component (empty particles of BPMV capsid protein). The bottom component particles contain ordered RNA in the same location as middle component. Although the ordered RNA density in both nucleoprotein particles is the average of the contents of 60 icosahedral asymmetric units, both nucleoprotein components show that the base density for the first two nucleotides is predominantly purine, while the next five appear to be predominantly pyrimidine. The empty capsid demonstrates that RNA dictates the order of the N-terminal 19 residues of the large subunit because these residues are invisible in the top component.
-Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus.,Lin T, Cavarelli J, Johnson JE Virology. 2003 Sep 15;314(1):26-33. PMID:14517057<ref>PMID:14517057</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Virus coat protein|Virus coat protein]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Viruses]]
+[[Category: Large Structures]]
-[[Category: Cavarelli, J]]
+[[Category: Cavarelli J]]
-[[Category: Johnson, J E]]
+[[Category: Johnson JE]]
-[[Category: Lin, T]]
+[[Category: Lin T]]
-[[Category: Comovirus]]
-[[Category: Icosahedral virus]]
-[[Category: Viral coat protein]]
-[[Category: Virus]]