2NNW

Alternative conformations of Nop56/58-fibrillarin complex and implication for induced-fit assenly of box C/D RNPs

Summary for 2NNW

• Entry DOI: 10.2210/pdb2nnw/pdb
• Descriptor: NOP5/NOP56 related protein, Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase (2 entities in total)
• Functional Keywords: box c/d, transferase
• Biological source: Pyrococcus furiosus; More
• Total number of polymer chains: 4
• Total formula weight: 140553.87

Authors

Oruganti, S.,Zhang, Y.,Terns, R.,Terns, M.P.,Li, H. (deposition date: 2006-10-24, release date: 2007-08-21, Last modification date: 2023-12-27)

Primary citation

Oruganti, S.,Zhang, Y.,Li, H.,Robinson, H.,Terns, M.P.,Terns, R.M.,Yang, W.,Li, H.
Alternative Conformations of the Archaeal Nop56/58-Fibrillarin Complex Imply Flexibility in Box C/D RNPs.
J.Mol.Biol., 371:1141-1150, 2007

PubMed Abstract: The Nop56/58-fibrillarin heterocomplex is a core protein complex of the box C/D ribonucleoprotein particles that modify and process ribosomal RNAs. The previous crystal structure of the Archaeoglobus fulgidus complex revealed a symmetric dimer of two Nop56/58-fibrillarin complexes linked by the coiled-coil domains of the Nop56/68 proteins. However, because the A. fulgidus Nop56/58 protein lacks some domains found in most other species, it was thought that the bipartite architecture of the heterocomplex was not likely a general phenomenon. Here we report the crystal structure of the Nop56/58-fibrillarin complex bound with methylation cofactor, S-adenosyl-L-methionine from Pyrococcus furiosus, at 2.7 A. The new complex confirms the generality of the previously observed bipartite arrangement. In addition however, the conformation of Nop56/58 in the new structure differs substantially from that in the earlier structure. The distinct conformations of Nop56/58 suggest potential flexibility in Nop56/58. Computational normal mode analysis supports this view. Importantly, fibrillarin is repositioned within the two complexes. We propose that hinge motion within Nop56/58 has important implications for the possibility of simultaneously positioning two catalytic sites at the two target sites of a bipartite box C/D guide RNA.

PubMed: 17617422
DOI: 10.1016/j.jmb.2007.06.029

Experimental method

X-RAY DIFFRACTION (2.7 Å)