1R6Z

The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes.

Song, J.J.Liu, J.Tolia, N.H.Schneiderman, J.Smith, S.K.Martienssen, R.A.Hannon, G.J.Joshua-Tor, L.

(2003) Nat Struct Biol 10: 1026-1032

  • DOI: 10.1038/nsb1016
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RISC, the RNA-induced silencing complex, uses short interfering RNAs (siRNAs) or micro RNAs (miRNAs) to select its targets in a sequence-dependent manner. Key RISC components are Argonaute proteins, which contain two characteristic domains, PAZ and P ...

    RISC, the RNA-induced silencing complex, uses short interfering RNAs (siRNAs) or micro RNAs (miRNAs) to select its targets in a sequence-dependent manner. Key RISC components are Argonaute proteins, which contain two characteristic domains, PAZ and PIWI. PAZ is highly conserved and is found only in Argonaute proteins and Dicer. We have solved the crystal structure of the PAZ domain of Drosophila Argonaute2. The PAZ domain contains a variant of the OB fold, a module that often binds single-stranded nucleic acids. PAZ domains show low-affinity nucleic acid binding, probably interacting with the 3' ends of single-stranded regions of RNA. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


    Organizational Affiliation

    Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera of Maltose-binding periplasmic protein and Argonaute 2
A, P, Z
509Escherichia coliDrosophila melanogaster
This entity is chimeric
Mutation(s): 0 
Gene Names: malEArgonaute 2 CG7439-PB
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Find proteins for Q9VUQ5 (Drosophila melanogaster)
Go to UniProtKB:  Q9VUQ5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download CCD File 
A, P, Z
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, P, Z
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MALKd:  10000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.227 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.811α = 90
b = 89.811β = 90
c = 380.326γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-16
    Changes: Refinement description, Source and taxonomy