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| | <StructureSection load='4k4x' size='340' side='right'caption='[[4k4x]], [[Resolution|resolution]] 2.37Å' scene=''> | | <StructureSection load='4k4x' size='340' side='right'caption='[[4k4x]], [[Resolution|resolution]] 2.37Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4k4x]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Cvb3 Cvb3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K4X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K4X FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4k4x]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Coxsackievirus_B3 Coxsackievirus B3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K4X FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.37Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ddk|3ddk]], [[3ol6|3ol6]], [[4k4s|4k4s]], [[4k4t|4k4t]], [[4k4u|4k4u]], [[4k4v|4k4v]], [[4k4w|4k4w]], [[4k4y|4k4y]], [[4k4z|4k4z]], [[4k50|4k50]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </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=4k4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4x OCA], [https://pdbe.org/4k4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k4x RCSB], [https://www.ebi.ac.uk/pdbsum/4k4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k4x ProSAT]</span></td></tr> |
| - | <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=4k4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k4x OCA], [http://pdbe.org/4k4x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4k4x RCSB], [http://www.ebi.ac.uk/pdbsum/4k4x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4k4x ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q66338_9ENTO Q66338_9ENTO]] Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).[SAAS:SAAS001676_004_016611] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[SAAS:SAAS000199_004_042266] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS001676_004_010047] | + | [https://www.uniprot.org/uniprot/Q5UEA2_9ENTO Q5UEA2_9ENTO] |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
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| - | RNA-dependent RNA polymerases play a vital role in the growth of RNA viruses where they are responsible for genome replication, but do so with rather low fidelity that allows for the rapid adaptation to different host cell environments. These polymerases are also a target for antiviral drug development. However, both drug discovery efforts and our understanding of fidelity determinants have been hampered by a lack of detailed structural information about functional polymerase-RNA complexes and the structural changes that take place during the elongation cycle. Many of the molecular details associated with nucleotide selection and catalysis were revealed in our recent structure of the poliovirus polymerase-RNA complex solved by first purifying and then crystallizing stalled elongation complexes. In the work presented here we extend that basic methodology to determine nine new structures of poliovirus, coxsackievirus, and rhinovirus elongation complexes at 2.2-2.9 A resolution. The structures highlight conserved features of picornaviral polymerases and the interactions they make with the template and product RNA strands, including a tight grip on eight basepairs of the nascent duplex, a fully pre-positioned templating nucleotide, and a conserved binding pocket for the +2 position template strand base. At the active site we see a pre-bound magnesium ion and there is conservation of a non-standard backbone conformation of the template strand in an interaction that may aid in triggering RNA translocation via contact with the conserved polymerase motif B. Moreover, by engineering plasticity into RNA-RNA contacts, we obtain crystal forms that are capable of multiple rounds of in-crystal catalysis and RNA translocation. Together, the data demonstrate that engineering flexible RNA contacts to promote crystal lattice formation is a versatile platform that can be used to solve the structures of viral RdRP elongation complexes and their catalytic cycle intermediates.
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| - | Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts.,Gong P, Kortus MG, Nix JC, Davis RE, Peersen OB PLoS One. 2013 May 8;8(5):e60272. doi: 10.1371/journal.pone.0060272. Print 2013. PMID:23667424<ref>PMID:23667424</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4k4x" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[RNA polymerase|RNA polymerase]] | + | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cvb3]] | + | [[Category: Coxsackievirus B3]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: RNA-directed RNA polymerase]]
| + | [[Category: Gong P]] |
| - | [[Category: Gong, P]] | + | [[Category: Peersen OB]] |
| - | [[Category: Peersen, O B]] | + | |
| - | [[Category: Polymerase]]
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| - | [[Category: Protein-rna complex]]
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| - | [[Category: Rna-dependent rna polymerase]]
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| - | [[Category: Transferase-rna complex]]
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