5uk4: Difference between revisions
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The | ==VESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1307== | ||
<StructureSection load='5uk4' size='340' side='right'caption='[[5uk4]], [[Resolution|resolution]] 3.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5uk4]] is a 44 chain structure with sequence from [https://en.wikipedia.org/wiki/Vesicular_stomatitis_Indiana_virus_strain_San_Juan Vesicular stomatitis Indiana virus strain San Juan] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UK4 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.204Å</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=5uk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uk4 OCA], [https://pdbe.org/5uk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uk4 RCSB], [https://www.ebi.ac.uk/pdbsum/5uk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uk4 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NCAP_VSIVA NCAP_VSIVA] Encapsidates the genome in a ratio of one N per nine ribonucleotides, protecting it from nucleases. The encapsidated genomic RNA is termed the NC and serves as template for transcription and replication. Replication is dependent on intracellular concentration of newly synthesized N, termed N(0), which corresponds to the protein not associated with RNA. In contrast, when associated with RNA, it is termed N. During replication, encapsidation by N(0) is coupled to RNA synthesis and all replicative products are resistant to nucleases (By similarity). | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The transcription and replication machinery of negative-stranded RNA viruses presents a possible target for interference in the viral life cycle. We demonstrate the validity of this concept through the use of cytosolically expressed single-domain antibody fragments (VHHs) that protect cells from a lytic infection with vesicular stomatitis virus (VSV) by targeting the viral nucleoprotein N. We define the binding sites for two such VHHs, 1004 and 1307, by X-ray crystallography to better understand their inhibitory properties. We found that VHH 1307 competes with the polymerase cofactor P for binding and thus inhibits replication and mRNA transcription, while binding of VHH 1004 likely only affects genome replication. The functional relevance of these epitopes is confirmed by the isolation of escape mutants able to replicate in the presence of the inhibitory VHHs. The escape mutations allow identification of the binding site of a third VHH that presumably competes with P for binding at another site than 1307. Collectively, these binding sites uncover different features on the N protein surface that may be suitable for antiviral intervention. | |||
Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication.,Hanke L, Schmidt FI, Knockenhauer KE, Morin B, Whelan SP, Schwartz TU, Ploegh HL EMBO Rep. 2017 Apr 10. pii: e201643764. doi: 10.15252/embr.201643764. PMID:28396572<ref>PMID:28396572</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5uk4" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Antibody 3D structures|Antibody 3D structures]] | |||
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]] | |||
*[[3D structures of non-human antibody|3D structures of non-human antibody]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Vesicular stomatitis Indiana virus strain San Juan]] | |||
[[Category: Vicugna pacos]] | |||
[[Category: Hanke L]] | |||
[[Category: Knockenhauer KE]] | |||
[[Category: Ploegh HL]] | |||
[[Category: Schwartz TU]] | |||
Latest revision as of 16:28, 4 October 2023
VESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1307VESICULAR STOMATITS VIRUS N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1307
Structural highlights
FunctionNCAP_VSIVA Encapsidates the genome in a ratio of one N per nine ribonucleotides, protecting it from nucleases. The encapsidated genomic RNA is termed the NC and serves as template for transcription and replication. Replication is dependent on intracellular concentration of newly synthesized N, termed N(0), which corresponds to the protein not associated with RNA. In contrast, when associated with RNA, it is termed N. During replication, encapsidation by N(0) is coupled to RNA synthesis and all replicative products are resistant to nucleases (By similarity). Publication Abstract from PubMedThe transcription and replication machinery of negative-stranded RNA viruses presents a possible target for interference in the viral life cycle. We demonstrate the validity of this concept through the use of cytosolically expressed single-domain antibody fragments (VHHs) that protect cells from a lytic infection with vesicular stomatitis virus (VSV) by targeting the viral nucleoprotein N. We define the binding sites for two such VHHs, 1004 and 1307, by X-ray crystallography to better understand their inhibitory properties. We found that VHH 1307 competes with the polymerase cofactor P for binding and thus inhibits replication and mRNA transcription, while binding of VHH 1004 likely only affects genome replication. The functional relevance of these epitopes is confirmed by the isolation of escape mutants able to replicate in the presence of the inhibitory VHHs. The escape mutations allow identification of the binding site of a third VHH that presumably competes with P for binding at another site than 1307. Collectively, these binding sites uncover different features on the N protein surface that may be suitable for antiviral intervention. Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication.,Hanke L, Schmidt FI, Knockenhauer KE, Morin B, Whelan SP, Schwartz TU, Ploegh HL EMBO Rep. 2017 Apr 10. pii: e201643764. doi: 10.15252/embr.201643764. PMID:28396572[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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