Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 183.09 kDa 
• Atom Count: 12,841 
• Modelled Residue Count: 1,458 
• Deposited Residue Count: 1,464 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 2F8T

Crystal structure of Aa-Ago with externally-bound siRNA

• PDB DOI: 10.2210/pdb2F8T/pdb
• NDB: PR0189

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-03 Released: 2006-10-31 
• Deposition Author(s): Yuan, Y.R., Chen, H.Y., Patel, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.297 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 

Literature

A Potential Protein-RNA Recognition Event along the RISC-Loading Pathway from the Structure of A. aeolicus Argonaute with Externally Bound siRNA.

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

(2006) Structure 14: 1557-1565

• PubMed: 17027504 
• DOI: 10.1016/j.str.2006.08.009
• Primary Citation of Related Structures:  
  2F8S, 2F8T


• PubMed 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.

---

Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Argonaute protein	C [auth A], D [auth B]	706	Aquifex aeolicus	Mutation(s): 0
UniProt
Find proteins for O67434 (Aquifex aeolicus (strain VF5)) Explore O67434  Go to UniProtKB:  O67434

Entity ID: 1
Molecule	Chains	Length	Organism	Image
26-MER	A [auth C], B [auth D]	26	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.297 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.2	α = 90
b = 118.077	β = 99.57
c = 98.498	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): Yuan, Y.R., Chen, H.Y., Patel, D.J.

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance