3raa: Difference between revisions

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-[[Image:3raa.jpg|left|200px]]
-<!--
+==Structural studies of AAV8 capsid transitions associated with endosomal trafficking==
-The line below this paragraph, containing "STRUCTURE_3raa", creates the "Structure Box" on the page.
+<StructureSection load='3raa' size='340' side='right'caption='[[3raa]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3raa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Adeno-associated_virus_-_8 Adeno-associated virus - 8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RAA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RAA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene></td></tr>
-{{STRUCTURE_3raa|  PDB=3raa  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3raa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3raa OCA], [https://pdbe.org/3raa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3raa RCSB], [https://www.ebi.ac.uk/pdbsum/3raa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3raa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8JQF8_9VIRU Q8JQF8_9VIRU]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The ssDNA parvoviruses enter host cells through receptor-mediated endocytosis and infection depends on processing in the early to late endosome as well as the lysosome prior to nuclear entry for replication. However, the mechanisms of capsid endosomal processing, including the effects of low pH, are poorly understood. To gain insight into the structural transitions required for this essential step in infection, the crystal structures of empty and GFP gene packaged Adeno-associated virus (AAV) serotype 8 (AAV8) has been determined at pHs 6.0, 5.5, and 4.0, and then at 7.5 after incubation at 4.0, mimicking the conditions encountered during endocytic trafficking. While the capsid viral protein (VP) topologies of all the structures were similar, significant amino acid side-chain conformational rearrangements were observed on (I) the interior surface of the capsid under the icosahedral three-fold axis near ordered nucleic acid density that was lost concomitant with the conformational change as pH was reduced and (II) the exterior capsid surface close to the icosahedral two-fold depression. The three-fold change is consistent with DNA release from an ordering interaction on the inside surface of the capsid at low pH and suggests transitions that likely trigger the capsid for genome uncoating. The surface change results in disruption of VP:VP interface interactions and a decrease in buried surface area between VP monomers. This disruption points to capsid destabilization which may (I) release VP1 amino acids for its phospholipase A2 function for endosomal escape and nuclear localization signals for nuclear targeting and (II) trigger genome uncoating.
-===Structural studies of AAV8 capsid transitions associated with endosomal trafficking===
+Structural studies of AAV8 capsid transitions associated with endosomal trafficking.,Nam HJ, Gurda BL, McKenna R, Potter M, Byrne B, Salganik M, Muzyczka N, Agbandje-McKenna M J Virol. 2011 Sep 7. PMID:21900159<ref>PMID:21900159</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3raa" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21900159}}, adds the Publication Abstract to the page
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21900159 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21900159}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Adeno-associated virus - 8]]
-[[3raa]] is a 1 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=3RAA OCA].
+[[Category: Large Structures]]
+[[Category: Agbandje-McKenna M]]
-==Reference==
+[[Category: Byrne B]]
-<ref group="xtra">PMID:021900159</ref><references group="xtra"/>
+[[Category: Gurda B]]
-[[Category: Viruses]]
+[[Category: McKenna R]]
-[[Category: Agbandje-McKenna, M.]]
+[[Category: Muzyczka N]]
-[[Category: Byrne, B.]]
+[[Category: Nam H-J]]
-[[Category: Gurda, B.]]
+[[Category: Porter M]]
-[[Category: McKenna, R.]]
+[[Category: Salganik M]]
-[[Category: Muzyczka, N.]]
-[[Category: Nam, H J.]]
-[[Category: Porter, M.]]
-[[Category: Salganik, M.]]
-[[Category: Beta barrel]]
-[[Category: Viral capsid]]
-[[Category: Virus]]