4gbt

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==Structural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles==
==Structural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles==
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<StructureSection load='4gbt' size='340' side='right' caption='[[4gbt]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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<StructureSection load='4gbt' size='340' side='right'caption='[[4gbt]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gbt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/H-1_parvovirus H-1 parvovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GBT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gbt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/H-1_parvovirus H-1 parvovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GBT 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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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]] 3.2&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4g0r|4g0r]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=4gbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gbt OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gbt RCSB], [http://www.ebi.ac.uk/pdbsum/4gbt PDBsum]</span></td></tr>
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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=4gbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gbt OCA], [https://pdbe.org/4gbt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gbt RCSB], [https://www.ebi.ac.uk/pdbsum/4gbt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gbt ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/CAPSD_PAVHH CAPSD_PAVHH]] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of two size variants of the capsid proteins, VP1 and VP2, which differ by the presence of an N-terminal extension in the minor protein VP1. The capsid encapsulates the genomic ssDNA. Capsid proteins are responsible for the attachment to host cell receptors. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptors also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus (By similarity).
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[https://www.uniprot.org/uniprot/CAPSD_PAVHH CAPSD_PAVHH] Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of two size variants of the capsid proteins, VP1 and VP2, which differ by the presence of an N-terminal extension in the minor protein VP1. The capsid encapsulates the genomic ssDNA. Capsid proteins are responsible for the attachment to host cell receptors. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptors also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus (By similarity).
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The structure of single-stranded DNA (ssDNA) packaging H-1 parvovirus (H-1PV), which is being developed as an antitumor gene delivery vector, has been determined for wild-type (wt) virions and noninfectious (empty) capsids to 2.7- and 3.2-A resolution, respectively, using X-ray crystallography. The capsid viral protein (VP) structure consists of an alpha-helix and an eight-stranded anti-parallel beta-barrel with large loop regions between the strands. The beta-barrel and loops form the capsid core and surface, respectively. In the wt structure, 600 nucleotides are ordered in an interior DNA binding pocket of the capsid. This accounts for approximately 12% of the H-1PV genome. The wt structure is identical to the empty capsid structure, except for side chain conformation variations at the nucleotide binding pocket. Comparison of the H-1PV nucleotides to those observed in canine parvovirus and minute virus of mice, two members of the genus Parvovirus, showed both similarity in structure and analogous interactions. This observation suggests a functional role, such as in capsid stability and/or ssDNA genome recognition for encapsulation. The VP structure differs from those of other parvoviruses in surface loop regions that control receptor binding, tissue tropism, pathogenicity, and antibody recognition, including VP sequences reported to determine tumor cell tropism for oncotropic rodent parvoviruses. These structures of H-1PV provide insight into structural features that dictate capsid stabilization following genome packaging and three-dimensional information applicable for rational design of tumor-targeted recombinant gene delivery vectors.
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Structural characterization of h-1 parvovirus: comparison of infectious virions to empty capsids.,Halder S, Nam HJ, Govindasamy L, Vogel M, Dinsart C, Salome N, McKenna R, Agbandje-McKenna M J Virol. 2013 May;87(9):5128-40. doi: 10.1128/JVI.03416-12. Epub 2013 Feb 28. PMID:23449783<ref>PMID:23449783</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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==See Also==
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</div>
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*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: H-1 parvovirus]]
[[Category: H-1 parvovirus]]
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[[Category: Agbandje-McKenna, M]]
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[[Category: Large Structures]]
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[[Category: Dinsart, C]]
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[[Category: Agbandje-McKenna M]]
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[[Category: Govindasamy, L]]
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[[Category: Dinsart C]]
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[[Category: Halder, S]]
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[[Category: Govindasamy L]]
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[[Category: McKenna, R]]
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[[Category: Halder S]]
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[[Category: Nam, H-J]]
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[[Category: McKenna R]]
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[[Category: Salome, N]]
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[[Category: Nam H-J]]
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[[Category: Vogel, M]]
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[[Category: Salome N]]
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[[Category: Beta-barrel]]
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[[Category: Vogel M]]
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[[Category: Capsid]]
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[[Category: Capsid protein]]
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[[Category: Icosahedral virus]]
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[[Category: Parvovirus]]
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[[Category: Virus]]
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Current revision

Structural characterization of H-1 Parvovirus: comparison of infectious virions to replication defective particles

PDB ID 4gbt

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