3nvk

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Current revision (10:01, 14 February 2024) (edit) (undo)
 
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<StructureSection load='3nvk' size='340' side='right'caption='[[3nvk]], [[Resolution|resolution]] 3.21&Aring;' scene=''>
<StructureSection load='3nvk' size='340' side='right'caption='[[3nvk]], [[Resolution|resolution]] 3.21&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3nvk]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NVK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3nvk]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NVK 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=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 3.209&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF0060 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), rpl7ae, PF1367 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), flpA, PF0059 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=SAM:S-ADENOSYLMETHIONINE'>SAM</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=3nvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvk OCA], [https://pdbe.org/3nvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nvk RCSB], [https://www.ebi.ac.uk/pdbsum/3nvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nvk ProSAT]</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=3nvk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvk OCA], [https://pdbe.org/3nvk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nvk RCSB], [https://www.ebi.ac.uk/pdbsum/3nvk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nvk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/FLPA_PYRFU FLPA_PYRFU]] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA (By similarity).[HAMAP-Rule:MF_00351] [[https://www.uniprot.org/uniprot/RL7A_PYRFU RL7A_PYRFU]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity).
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[https://www.uniprot.org/uniprot/Q8U4M1_PYRFU Q8U4M1_PYRFU]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) direct site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs and are critical for gene expression. Here we report crystal structures of an archaeal box C/D RNP containing three core proteins (fibrillarin, Nop56/58, and L7Ae) and a half-mer box C/D guide RNA paired with a substrate RNA. The structure reveals a guide-substrate RNA duplex orientation imposed by a composite protein surface and the conserved GAEK motif of Nop56/58. Molecular modeling supports a dual C/D RNP structure that closely mimics that recently visualized by electron microscopy. The substrate-bound dual RNP model predicts an asymmetric protein distribution between the RNP that binds and methylates the substrate RNA. The predicted asymmetric nature of the holoenzyme is consistent with previous biochemical data on RNP assembly and provides a simple solution for accommodating base-pairing between the C/D guide RNA and large ribosomal and spliceosomal substrate RNAs.
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Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.,Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H Mol Cell. 2010 Sep 24;39(6):939-49. PMID:20864039<ref>PMID:20864039</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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</div>
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<div class="pdbe-citations 3nvk" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Ribosomal protein L7/L12|Ribosomal protein L7/L12]]
*[[Ribosomal protein L7/L12|Ribosomal protein L7/L12]]
*[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
*[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Pyrfu]]
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[[Category: Pyrococcus furiosus DSM 3638]]
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[[Category: Li, H]]
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[[Category: Li H]]
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[[Category: Wang, R]]
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[[Category: Wang R]]
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[[Category: Xue, S]]
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[[Category: Xue S]]
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[[Category: Nop domain kink turn methyl transferase]]
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[[Category: Ribosome biogenesis spliceosome biogenesis]]
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[[Category: Transferase-rna complex]]
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Current revision

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle

PDB ID 3nvk

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