6y6k

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<StructureSection load='6y6k' size='340' side='right'caption='[[6y6k]], [[Resolution|resolution]] 3.78&Aring;' scene=''>
<StructureSection load='6y6k' size='340' side='right'caption='[[6y6k]], [[Resolution|resolution]] 3.78&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6y6k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y6K FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6y6k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/SFTS_virus_AH12 SFTS virus AH12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y6K FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">Electron Microscopy, [[Resolution|Resolution]] 3.78&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6xya|6xya]]</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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6k OCA], [http://pdbe.org/6y6k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y6k RCSB], [http://www.ebi.ac.uk/pdbsum/6y6k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6k ProSAT]</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=6y6k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6k OCA], [https://pdbe.org/6y6k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y6k RCSB], [https://www.ebi.ac.uk/pdbsum/6y6k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6k ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
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[https://www.uniprot.org/uniprot/L_SFTS L_SFTS]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 A or better shows significant improvement of the models and of the fit of these models to the target maps.
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The Bunyavirales order contains several emerging viruses with high epidemic potential, including Severe fever with thrombocytopenia syndrome virus (SFTSV). The lack of medical countermeasures, such as vaccines and antivirals, is a limiting factor for the containment of any virus outbreak. To develop such antivirals a profound understanding of the viral replication process is essential. The L protein of bunyaviruses is a multi-functional and multi-domain protein performing both virus transcription and genome replication and, therefore, is an ideal drug target. We established expression and purification procedures for the full-length L protein of SFTSV. By combining single-particle electron cryo-microscopy and X-ray crystallography, we obtained 3D models covering approximately 70% of the SFTSV L protein in the apo-conformation including the polymerase core region, the endonuclease and the cap-binding domain. We compared this first L structure of the Phenuiviridae family to the structures of La Crosse peribunyavirus L protein and influenza orthomyxovirus polymerase. Together with a comprehensive biochemical characterization of the distinct functions of SFTSV L protein, this work provides a solid framework for future structural and functional studies of L protein-RNA interactions and the development of antiviral strategies against this group of emerging human pathogens.
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Real-space refinement in PHENIX for cryo-EM and crystallography.,Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):531-544. doi:, 10.1107/S2059798318006551. Epub 2018 May 30. PMID:29872004<ref>PMID:29872004</ref>
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Structural and functional characterization of the severe fever with thrombocytopenia syndrome virus L protein.,Vogel D, Thorkelsson SR, Quemin ERJ, Meier K, Kouba T, Gogrefe N, Busch C, Reindl S, Gunther S, Cusack S, Grunewald K, Rosenthal M Nucleic Acids Res. 2020 Apr 20. pii: 5822961. doi: 10.1093/nar/gkaa253. PMID:32313945<ref>PMID:32313945</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Busch, C]]
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[[Category: SFTS virus AH12]]
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[[Category: Cusack, S]]
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[[Category: Busch C]]
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[[Category: Gogrefe, N]]
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[[Category: Cusack S]]
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[[Category: Gruenewald, K]]
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[[Category: Gogrefe N]]
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[[Category: Guenther, S]]
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[[Category: Gruenewald K]]
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[[Category: Kouba, T]]
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[[Category: Guenther S]]
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[[Category: Meier, K]]
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[[Category: Kouba T]]
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[[Category: Quemin, E]]
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[[Category: Meier K]]
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[[Category: Reindl, S]]
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[[Category: Quemin E]]
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[[Category: Rosenthal, M]]
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[[Category: Reindl S]]
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[[Category: Thorkelsson, S R]]
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[[Category: Rosenthal M]]
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[[Category: Vogel, D]]
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[[Category: Thorkelsson SR]]
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[[Category: Bunyavirus]]
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[[Category: Vogel D]]
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[[Category: Cap-snatching]]
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[[Category: L protein]]
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[[Category: Phenuiviridae]]
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[[Category: Viral polymerase]]
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[[Category: Viral protein]]
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Current revision

Cryo-EM structure of a Phenuiviridae L protein

PDB ID 6y6k

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