PDBsum entry: 1r6z

Gene regulation

PDB id: 1r6z

Contents

Protein chains

498 a.a. *

Ligands

MAL ×3

Metals

_NI ×9

Waters ×57

* Residue conservation analysis

PDB id:

1r6z

Name:

Gene regulation

Title:

The crystal structure of the argonaute2 paz domain (as a mbp

Structure:

Chimera of maltose-binding periplasmic protein an argonaute 2. Chain: p, a, z. Fragment: mbp (residues 28-392) fused with argonaute2 paz d (residues 591-726). Synonym: maltodextrin-binding protein, mmbp, cg7439-pb. Engineered: yes. Other_details: the construct is a fusion of e.Coli mbp (res 392) and d.Melanogaster argonaute2 paz domain (residues 59

Source:

Escherichia coli, drosophila melanogas , fruit fly. Organism_taxid: 562,7227. Strain: ,. Gene: male, argonaute 2 cg7439-pb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.227 R-free: 0.281

Authors:

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

Key ref:

J.J.Song et al. (2003). The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat Struct Biol, 10, 1026-1032. PubMed id: 14625589 DOI: 10.1038/nsb1016

Date:

17-Oct-03 Release date: 13-Jan-04

Protein chains

P0AEX9  (MALE_ECOLI) -  Maltose-binding periplasmic protein

Seq: 396 a.a.

Struc: 498 a.a.*

Protein chains

Q9VUQ5  (AGO2_DROME) -  Protein argonaute-2

Seq: 1214 a.a.

Struc: 498 a.a.*

* PDB and UniProt seqs differ at 351 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: periplasmic space (2 terms)
• Biological process: transport (4 terms)
• Biochemical function: transporter activity (5 terms)

DOI no: 10.1038/nsb1016

Nat Struct Biol 10:1026-1032 (2003)

PubMed id: 14625589

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

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

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 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.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of Ago2-PAZ. (a) Stereo diagram of the C trace of Ago2-PAZ. This figure and Figures 2a, 4c and 5a were prepared with BobScript28, MolScript29, and Raster3D^30, 31. (b) A portion of the final 2F[o] - F[c] electron density map around the invariant aromatic residues at the back of the cleft (see below), contoured at 1 , superimposed on the refined model, drawn in stick representation. (c) Stereo ribbon diagram of the Ago2-PAZ domain with -strands in purple and -helices in blue. The intersubdomain cleft is apparent in this view shown in a view 90° from a.

Figure 2.
Figure 2. Ago2-PAZ has a deviant OB fold. A topology diagram for Ago2-PAZ on the right and aspartyl-tRNA synthetase^32 on the left depicting the differences in the topology of the -barrels.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 1026-1032) copyright 2003.

Figures were selected by an automated process.