› 4ngf

X-ray diffraction
3.1Å resolution

Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 17-mer siRNA having 5'-p and UU-3' ends (3.1 Angstrom resolution)

Released:
DOI: 10.2210/pdb4ngf/pdb
PDB entry 4ngf coloured by chain, front view.
PDB entry 4ngf coloured by chain, side view.
PDB entry 4ngf 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-194044 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Endoribonuclease Dicer Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 302 amino acids
Theoretical weight: 35.04 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*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3' Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 17 nucleotides
Theoretical weight: 5.36 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: C2221
Unit cell:
a: 99.245Å b: 104.191Å c: 368.64Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.223 0.27
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

26 review citations

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

4 mentions without citation

A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer.
Tian et al. (2014)
3 more