4NGD

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)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.958 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer.

Tian, Y.Simanshu, D.K.Ma, J.B.Park, J.E.Heo, I.Kim, V.N.Patel, D.J.

(2014) Mol.Cell 53: 606-616

  • DOI: 10.1016/j.molcel.2014.01.003
  • Primary Citation of Related Structures:  

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoribonuclease Dicer
A
302Homo sapiensMutation(s): 2 
Gene Names: DICER1 (DICER, HERNA, KIAA0928)
EC: 3.1.26.3
Find proteins for Q9UPY3 (Homo sapiens)
Go to Gene View: DICER1
Go to UniProtKB:  Q9UPY3
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'B12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.958 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.710α = 90.00
b = 84.621β = 113.33
c = 51.364γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-03-12
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description