4NH3: Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 13-mer siRNA having 5'-pU and UU-3' ends (2.6 Angstrom resolution)

Citation:
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 alpha-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.
PDB ID: 4NH3Download
MMDB ID: 118062
PDB Deposition Date: 2013/11/4
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.616  Å
Source Organism:
Homo sapiens
Similar Structures:
Biological Unit for 4NH3: trimeric; determined by author
Molecular Components in 4NH3
Label Count Molecule
Protein (1 molecule)
1
Endoribonuclease Dicer(Gene symbol: DICER1)
Molecule annotation
Nucleotide(1 molecule)
2
5'-r(p*up*gp*cp*gp*ap*ap*up*up*cp*gp*cp*up*u)-3'
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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