3nvk | pdb_00003nvk

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

spinqualitylabelsall models 3nvk, resolution 3.21Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3nvk is a 10 chain structure with sequence from Pyrfu. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: SAM Gene: PF0060 (PYRFU), rpl7ae, PF1367 (PYRFU), flpA, PF0059 (PYRFU) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [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] [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). 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Kink-turn motif Ribosomal protein L7/L12 User:Wayne Decatur/kink-turn motif

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