3BW1

Crystal structure of homomeric yeast Lsm3 exhibiting novel octameric ring organisation

Summary for 3BW1

• Entry DOI: 10.2210/pdb3bw1/pdb
• Related: 1B34 1D3B 1I81 1N9R 1N9S
• Descriptor: U6 snRNA-associated Sm-like protein LSm3, (4S)-2-METHYL-2,4-PENTANEDIOL, SULFATE ION, ... (4 entities in total)
• Functional Keywords: rna-binding protein, sm-like protein, sm protein, ring, homomeric, octamer, mrna processing, mrna splicing, nucleus, ribonucleoprotein, rrna processing, trna processing, rna binding protein
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 2
• Total formula weight: 22567.43

Authors

Naidoo, N.,Harrop, S.J.,Curmi, P.M.G.,Mabbutt, B.C. (deposition date: 2008-01-07, release date: 2008-03-25, Last modification date: 2023-11-01)

Primary citation

Naidoo, N.,Harrop, S.J.,Sobti, M.,Haynes, P.A.,Szymczyna, B.R.,Williamson, J.R.,Curmi, P.M.G.,Mabbutt, B.C.
Crystal structure of Lsm3 octamer from Saccharomyces cerevisiae: implications for Lsm ring organisation and recruitment
J.Mol.Biol., 377:1357-1371, 2008

PubMed Abstract: Sm and Sm-like (Lsm) proteins are core components of the ribonucleoprotein complexes essential to key nucleic acid processing events within the eukaryotic cell. They assemble as polyprotein ring scaffolds that have the capacity to bind RNA substrates and other necessary protein factors. The crystal structure of yeast Lsm3 reveals a new organisation of the L/Sm beta-propeller ring, containing eight protein subunits. Little distortion of the characteristic L/Sm fold is required to form the octamer, indicating that the eukaryotic Lsm ring may be more pliable than previously thought. The homomeric Lsm3 octamer is found to successfully recruit Lsm6, Lsm2 and Lsm5 directly from yeast lysate. Our crystal structure shows the C-terminal tail of each Lsm3 subunit to be engaged in connections across rings through specific beta-sheet interactions with elongated loops protruding from neighbouring octamers. While these loops are of distinct length for each Lsm protein and generally comprise low-complexity polar sequences, several Lsm C-termini comprise hydrophobic sequences suitable for beta-sheet interactions. The Lsm3 structure thus provides evidence for protein-protein interactions likely utilised by the highly variable Lsm loops and termini in the recruitment of RNA processing factors to mixed Lsm ring scaffolds. Our coordinates also provide updated homology models for the active Lsm[1-7] and Lsm[2-8] heptameric rings.

PubMed: 18329667
DOI: 10.1016/j.jmb.2008.01.007

Experimental method

X-RAY DIFFRACTION (2.5 Å)