This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3nvm

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3nvm"

Categories: Large Structures | Pyrococcus furiosus DSM 3638 | Li H | Wang R | Xue S

@@ Line 3: / Line 3: @@
 <StructureSection load='3nvm' size='340' side='right'caption='[[3nvm]], [[Resolution|resolution]] 3.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3nvm]] is a 2 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=3NVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NVM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3nvm]] is a 2 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=3NVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NVM FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3nmu|3nmu]], [[3nvi|3nvi]], [[3nvk|3nvk]]</div></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]] 3.408&#8491;</td></tr>
-<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]), flpA, PF0059 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3nvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvm OCA], [https://pdbe.org/3nvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nvm RCSB], [https://www.ebi.ac.uk/pdbsum/3nvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nvm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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/Q8U4M1_PYRFU Q8U4M1_PYRFU]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3nvm" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Kink-turn motif|Kink-turn motif]]
 *[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pyrfu]]
+[[Category: Pyrococcus furiosus DSM 3638]]
-[[Category: Li, H]]
+[[Category: Li H]]
-[[Category: Wang, R]]
+[[Category: Wang R]]
-[[Category: Xue, S]]
+[[Category: Xue S]]
-[[Category: Methyltransferase]]
-[[Category: Nop domain]]
-[[Category: Ribosome biogenesis]]
-[[Category: Spliceosome biogenesis]]
-[[Category: Transferase]]

3nvm

From Proteopedia

Current revision

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

Structural highlights

Function

See Also

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox