› 4ngd

X-ray diffraction
1.96Å resolution

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)

Released:
DOI: 10.2210/pdb4ngd/pdb
PDB entry 4ngd coloured by chain, front view.
PDB entry 4ngd coloured by chain, side view.
PDB entry 4ngd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer.
Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ
Mol Cell 53 606-16 (2014)
PMID: 24486018

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-219673 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Endoribonuclease Dicer Chain: A
Molecule details ›
Chain: A
Length: 302 amino acids
Theoretical weight: 34.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UPY3 (Residues: 765-1065; Coverage: 16%)
Gene names: DICER, DICER1, HERNA, KIAA0928
Sequence domains:
Structure domains: paz domain
5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.79 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2
Unit cell:
a: 108.71Å b: 84.621Å c: 51.364Å
α: 90° β: 113.33° γ: 90°
R-values:
R R work R free
0.178 0.177 0.204
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

25 review citations

Regulation of microRNA biogenesis.
Ha et al. (2014)
24 more

5 mentions without citation

A Glimpse of "Dicer Biology" Through the Structural and Functional Perspective.
Paturi et al. (2021)
4 more