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

Area of Science:

• Molecular Biology
• Structural Biology
• Biochemistry

Background:

• Box C/D small nucleolar and Cajal body ribonucleoprotein particles (sno/scaRNPs) are essential for site-specific 2'-O-methylation of ribosomal and spliceosomal RNAs.
• These modifications are critical for proper gene expression and cellular function.

Purpose of the Study:

• To determine the crystal structures of an archaeal box C/D RNP bound to a guide RNA and a substrate RNA.
• To elucidate the structural basis for guide-substrate RNA duplex formation and methylation by the RNP.

Main Methods:

• X-ray crystallography was used to obtain high-resolution structures of the archaeal box C/D RNP complex.
• Molecular modeling was employed to support and extend the structural findings, including the prediction of a dual RNP structure.

Main Results:

• Crystal structures revealed the orientation of a guide-substrate RNA duplex, dictated by a composite protein surface and the Nop56/58 GAEK motif.
• Molecular modeling supported a dual RNP model, mimicking recent electron microscopy observations.
• The substrate-bound dual RNP model predicts an asymmetric protein distribution, consistent with biochemical data.

Conclusions:

• The revealed structure provides a molecular understanding of how box C/D RNPs bind and orient substrate RNAs for 2'-O-methylation.
• The predicted asymmetric holoenzyme structure offers a mechanism for accommodating large substrate RNAs during methylation.
• These findings advance our knowledge of the fundamental mechanisms governing RNA modification and gene expression.