5uf6: Difference between revisions

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<SX load='5uf6' size='340' side='right' viewer='molstar' caption='[[5uf6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<SX load='5uf6' size='340' side='right' viewer='molstar' caption='[[5uf6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5uf6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Adeno-associated_virus Adeno-associated virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UF6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NTO:TRISULFOAMINO+HEPARIN+PENTASACCHARIDE'>NTO</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CAPSID ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272636 Adeno-associated virus])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDP:BETA-D-GLUCOPYRANURONIC+ACID'>BDP</scene>, <scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=PRD_900028:fondaparinux'>PRD_900028</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</scene>, <scene name='pdbligand=SUS:2-DEOXY-3,6-DI-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE'>SUS</scene>, <scene name='pdbligand=ZDO:methyl+2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside'>ZDO</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [http://pdbe.org/5uf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 ProSAT]</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=5uf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uf6 OCA], [https://pdbe.org/5uf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uf6 RCSB], [https://www.ebi.ac.uk/pdbsum/5uf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uf6 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Atomic structures of adeno-associated virus (AAV)-DJ, alone and in complex with fondaparinux, have been determined by cryoelectron microscopy at 3 A resolution. The gene therapy vector, AAV-DJ, is a hybrid of natural serotypes that was previously derived by directed evolution, selecting for hepatocyte entry and resistance to neutralization by human serum. The structure of AAV-DJ differs from that of parental serotypes in two regions where neutralizing antibodies bind, so immune escape appears to have been the primary driver of AAV-DJ's directed evolution. Fondaparinux is an analog of cell surface heparan sulfate to which several AAVs bind during entry. Fondaparinux interacts with viral arginines at a known heparin binding site, without the large conformational changes whose presence was controversial in low-resolution imaging of AAV2-heparin complexes. The glycan density suggests multi-modal binding that could accommodate sequence variation and multivalent binding along a glycan polymer, consistent with a role in attachment, prior to more specific interactions with a receptor protein mediating entry.


The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparinoid Pentasaccharide.,Xie Q, Spear JM, Noble AJ, Sousa DR, Meyer NL, Davulcu O, Zhang F, Linhardt RJ, Stagg SM, Chapman MS Mol Ther Methods Clin Dev. 2017 Mar 8;5:1-12. doi: 10.1016/j.omtm.2017.02.004., eCollection 2017 Jun 16. PMID:28480299<ref>PMID:28480299</ref>
==See Also==
 
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5uf6" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</SX>
</SX>
[[Category: Adeno-associated virus]]
[[Category: Adeno-associated virus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chapman, M]]
[[Category: Chapman M]]
[[Category: Davulcu, O]]
[[Category: Davulcu O]]
[[Category: Linhardt, R J]]
[[Category: Linhardt RJ]]
[[Category: Meyer, N L]]
[[Category: Meyer NL]]
[[Category: Noble, A J]]
[[Category: Noble AJ]]
[[Category: Sousa, D R]]
[[Category: Sousa DR]]
[[Category: Spear, J M]]
[[Category: Spear JM]]
[[Category: Stagg, S M]]
[[Category: Stagg SM]]
[[Category: Xie, Q]]
[[Category: Xie Q]]
[[Category: Zhang, F]]
[[Category: Zhang F]]
[[Category: Attachment]]
[[Category: Glycan]]
[[Category: Receptor]]
[[Category: Virus like particle]]

Latest revision as of 17:26, 6 March 2024

The 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid PentasaccharideThe 2.8 A Electron Microscopy Structure of Adeno-Associated Virus-DJ Bound by a Heparanoid Pentasaccharide

5uf6, resolution 2.80Å

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OCA
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