SNAP output for PDB entry 4ngd [SNAP web server]

PDB-id

4ngd; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase-RNA

Method

X-ray (1.958 Å)

Summary

Structure of human dicer platform-paz-connector helix cassette in complex with 12-mer sirna having 5'-p and uu-3' ends (1.95 angstrom resolution)

Reference

Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ (2014): "A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer." Mol.Cell, 53, 606-616. doi: 10.1016/j.molcel.2014.01.003.

Abstract

We have solved two families of crystal structures of the human Dicer "platform-PAZ-connector helix" cassette in complex with small interfering RNAs (siRNAs). The structures possess two adjacently positioned pockets: a 2 nt 3'-overhang-binding pocket within the PAZ domain (3' pocket) and a phosphate-binding pocket within the platform domain (phosphate pocket). One family of complexes contains a knob-like α-helical protrusion, designated "hDicer-specific helix," that separates the two pockets and orients the bound siRNA away from the surface of Dicer, which could be indicative of a product release/transfer state. In the second complex, the helical protrusion is melted/disordered and the bound siRNA is aligned toward the surface of Dicer, suggestive of a cleavage-competent state. These structures allow us to propose that the transition from the cleavage-competent to the postulated product release/transfer state may involve release of the 5'-phosphate from the phosphate pocket while retaining the 3' overhang in the 3' pocket.