6jim: Difference between revisions

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<StructureSection load='6jim' size='340' side='right'caption='[[6jim]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='6jim' size='340' side='right'caption='[[6jim]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6jim]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chikv Chikv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JIM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JIM FirstGlance]. <br>
<table><tr><td colspan='2'>[[6jim]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chikungunya_virus Chikungunya virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JIM FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AL:ALUMINUM+ION'>AL</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <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&#8491;</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=6jim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jim OCA], [http://pdbe.org/6jim PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jim RCSB], [http://www.ebi.ac.uk/pdbsum/6jim PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jim ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AL:ALUMINUM+ION'>AL</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6jim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jim OCA], [https://pdbe.org/6jim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jim RCSB], [https://www.ebi.ac.uk/pdbsum/6jim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jim ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A076V769_9VIRU A0A076V769_9VIRU] Inactive precursor of the viral replicase, which is activated by cleavages carried out by the viral protease nsP2.[ARBA:ARBA00002589]
Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Here, we report the crystal structure of the nsP2h bound to the conserved 3'-end 14 nucleotides of the CHIKV genome and the nonhydrolyzable transition-state nucleotide analog ADP-AlF4 Overall, the structural analysis revealed that nsP2h adopts a uniquely folded N-terminal domain followed by a superfamily 1 RNA helicase fold. The conserved helicase motifs establish polar contacts with the RNA backbone. There are three hydrophobic residues (Y161, F164, and F287) which form stacking interactions with RNA bases and thereby bend the RNA backbone. An F287A substitution that disrupted these stacking interactions increased the basal ATPase activity but decreased the RNA binding affinity. Furthermore, the F287A substitution reduced viral infectivity by attenuating subgenomic RNA synthesis. Replication of the mutant virus was restored by pseudoreversion (A287V) or adaptive mutations in the RecA2 helicase domain (T358S or V410I). Y161A and/or F164A substitutions, which were designed to disrupt the interactions with the RNA molecule, did not affect the ATPase activity but completely abolished the replication and transcription of viral RNA and the infectivity of CHIKV. Our study sheds light on the roles of the RNA helicase region in viral replication and provides insights that might be applicable to alphaviruses and other RNA viruses in general.


Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase.,Law YS, Utt A, Tan YB, Zheng J, Wang S, Chen MW, Griffin PR, Merits A, Luo D Proc Natl Acad Sci U S A. 2019 Apr 18. pii: 1900656116. doi:, 10.1073/pnas.1900656116. PMID:31000599<ref>PMID:31000599</ref>
==See Also==
 
*[[Helicase 3D structures|Helicase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
*[[Nonstructural protein 3D structures|Nonstructural protein 3D structures]]
</div>
<div class="pdbe-citations 6jim" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Chikv]]
[[Category: Chikungunya virus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Law, Y S]]
[[Category: Law YS]]
[[Category: Helicase]]
[[Category: Viral protein-rna complex]]

Latest revision as of 13:38, 27 March 2024

Viral helicase proteinViral helicase protein

Structural highlights

6jim is a 4 chain structure with sequence from Chikungunya virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A076V769_9VIRU Inactive precursor of the viral replicase, which is activated by cleavages carried out by the viral protease nsP2.[ARBA:ARBA00002589]

See Also

6jim, resolution 2.00Å

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