2FFL

Crystal Structure of Dicer from Giardia intestinalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Double-Stranded RNA Processing by Dicer

MacRae, I.J.Zhou, K.Li, F.Repic, A.Brooks, A.N.Cande, W.Z.Adams, P.D.Doudna, J.A.

(2006) Science 311: 195-198

  • DOI: 10.1126/science.1121638
  • Primary Citation of Related Structures:  
    2FFL

  • PubMed Abstract: 
  • The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface ...

    The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DicerA, B, C, D756Giardia intestinalisMutation(s): 0 
EC: 3.1.26.3 (PDB Primary Data), 3.1.26 (UniProt)
UniProt
Find proteins for A8BQJ3 (Giardia intestinalis (strain ATCC 50803 / WB clone C6))
Explore A8BQJ3 
Go to UniProtKB:  A8BQJ3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , E [auth A] , EA [auth C] , F [auth A] , FA [auth C] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  E [auth A],  EA [auth C],  F [auth A],  FA [auth C],  G [auth A],  GA [auth C],  H [auth A],  HA [auth C],  I [auth A],  IA [auth C],  J [auth A],  JA [auth D],  K [auth A],  KA [auth D],  L [auth A],  LA [auth D],  M [auth A],  MA [auth D],  N [auth A],  NA [auth D],  O [auth A],  OA [auth D],  P [auth A],  PA [auth D],  Q [auth B],  QA [auth D],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Y [auth B],  Z [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.515α = 90
b = 174.101β = 90
c = 152.91γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description