PDBsum entry 2f8s

RNA binding protein/RNA

PDB id: 2f8s

Contents

Protein chains

704 a.a. *

DNA/RNA

Waters ×30

* Residue conservation analysis

PDB id:

2f8s

Name:

RNA binding protein/RNA

Title:

Crystal structure of aa-ago with externally-bound sirna

Structure:

5'-r(p Ap Gp Ap Cp Ap Gp Cp Ap Up Ap Up Ap Up Gp Cp Up Gp U p Cp Up Up U)-3'. Chain: c, d. Engineered: yes. Argonaute protein. Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Trimer (from PQS)

Resolution:

3.00Å R-factor: 0.217 R-free: 0.307

Authors:

Y.R.Yuan,H.Y.Chen,D.J.Patel

Key ref:

Y.R.Yuan et al. (2006). A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA. Structure, 14, 1557-1565. PubMed id: 17027504 DOI: 10.1016/j.str.2006.08.009

Date:

03-Dec-05 Release date: 31-Oct-06

Protein chains

O67434  (O67434_AQUAE) -  Protein argonaute from Aquifex aeolicus (strain VF5)

Seq: 706 a.a.

Struc: 704 a.a.

DNA/RNA chains

A-G-A-C-A-G-C-A-U-A-U-A-U-G-C-U-G-U-C-U-U-U 22 bases

A-G-A-C-A-G-C-A-U-A-U-A-U-G-C-U-G-U-C-U-U-U 22 bases

Enzyme reactions

• Enzyme class: E.C.3.1.26.- - ?????

DOI no: 10.1016/j.str.2006.08.009

Structure 14:1557-1565 (2006)

PubMed id: 17027504

A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA.

Y.R.Yuan, Y.Pei, H.Y.Chen, T.Tuschl, D.J.Patel.

ABSTRACT

Argonaute proteins are key components of the RNA-induced silencing complex (RISC). They provide both architectural and catalytic functionalities associated with small interfering RNA (siRNA) guide strand recognition and subsequent guide strand-mediated cleavage of complementary mRNAs. We report on the 3.0 A crystal structures of 22-mer and 26-mer siRNAs bound to Aquifex aeolicus Argonaute (Aa-Ago), where one 2 nt 3' overhang of the siRNA inserts into a cavity positioned on the outer surface of the PAZ-containing lobe of the bilobal Aa-Ago architecture. The first overhang nucleotide stacks over a tyrosine ring, while the second overhang nucleotide, together with the intervening sugar-phosphate backbone, inserts into a preformed surface cavity. Photochemical crosslinking studies on Aa-Ago with 5-iodoU-labeled single-stranded siRNA and siRNA duplex provide support for this externally bound siRNA-Aa-Ago complex. The structure and biochemical data together provide insights into a protein-RNA recognition event potentially associated with the RISC-loading pathway.

Selected figure(s)

Figure 2.
Figure 2. Detailed Views of Specific Protein-RNA Interactions in the Complex between 22-mer siRNA and Aa-Ago
(A) A stereoview of interactions between the 2 nt overhang at one end of the externally bound 22-mer siRNA and the outer surface of the PAZ-containing lobe (pink-colored N and cyan-colored PAZ domains; green-colored L1 and yellow-colored L2 linkers) of Aa-Ago (cyan-colored in Figure 1A). The overhang base U21 stacks on the aromatic ring of orange-colored Y119, which is highly conserved among bacterial Agos, while the overhang base U22 is inserted into a cavity whose walls involve segments from α2 of the N domain, α3 from the L1 linker, and loops from the PAZ domain. Further, A1 and U20 of the terminal A1•U20 base pair stack on the side chain of orange-colored R123 and the U21 base, respectively.
(B) Ribbon representation of the outward-pointing face of the PAZ-containing lobe of the cyan-colored Aa-Ago (Figure 1A); the bound 2 nt 3′ overhang is shown in a stick representation. The color coding of domains and linkers is as in (A). The bound 2 nt overhang segment is shown in a stick representation.
(C) Surface representation of the PAZ-containing lobe as in (B); the bound 2 nt overhang segment is shown in space-filling representation.

Figure 3.
Figure 3. Crystal Structure of the Complex between 22-mer siRNA and Aa-Ago
(A) A view of the crystal structure of the complex between externally bound 22-mer siRNA and Aa-Ago. The color codes of the various domains and linkers of Aa-Ago are as follows: N domain, pink; L1 linker, green; PAZ domain, cyan; L2 linker, yellow; Mid domain, pink; PIWI domain, cyan; and PIWI box, red. The siRNA is shown in beige, except for the 2 nt overhang at one end, which is colored red. The backbone phosphorus atoms are colored yellow.
(B) The view in (A) rotated by 90° along the z axis.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1557-1565) copyright 2006.

Figures were selected by an automated process.