1YVU

Crystal structure of A. aeolicus Argonaute

• PDB DOI: https://doi.org/10.2210/pdb1YVU/pdb

• Classification: RNA BINDING PROTEIN, GENE REGULATION
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-02-16 Released: 2005-08-09 
• Deposition Author(s): Yuan, Y.R., Pei, Y., Ma, J.B., Kuryavyi, V., Zhadina, M., Meister, G., Chen, H.Y., Dauter, Z., Tuschl, T., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.298 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Crystal structure of A. aeolicus Argonaute provides unique perspectives into the mechanism of guide strand-mediated mRNA cleavage

Yuan, Y.R., Pei, Y., Ma, J.B., Kuryavyi, V., Zhadina, M., Meister, G., Chen, H.Y., Dauter, Z., Tuschl, T., Patel, D.J.

(2005) Mol Cell 19: 405-419

• PubMed: 16061186 
• DOI: https://doi.org/10.1016/j.molcel.2005.07.011
• Primary Citation of Related Structures:  
  1YVU


• PubMed Abstract: 
  

  Argonaute (Ago) proteins constitute a key component of the RNA-induced silencing complex (RISC). We report the crystal structure of Aquifex aeolicus Ago (Aa-Ago) together with binding and cleavage studies, which establish this eubacterial Ago as a bona fide guide DNA strand-mediated site-specific RNA endonuclease. We have generated a stereochemically robust model of the complex, where the guide DNA-mRNA duplex is positioned within a basic channel spanning the bilobal interface, such that the 5' phosphate of the guide strand can be anchored in a basic pocket, and the mRNA can be positioned for site-specific cleavage by RNase H-type divalent cation-coordinated catalytic Asp residues of the PIWI domain. Domain swap experiments involving chimeras of human Ago (hAgo1) and cleavage-competent hAgo2 reinforce the role of the PIWI domain in "slicer" activity. We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83.59 kDa 
• Atom Count: 5,740 
• Modelled Residue Count: 682 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein aq_1447	A	706	Aquifex aeolicus VF5	Mutation(s): 6
UniProt
Find proteins for O67434 (Aquifex aeolicus (strain VF5)) Explore O67434  Go to UniProtKB:  O67434

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.298 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.15	α = 90
b = 100.679	β = 90
c = 115.217	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-09 
Deposition Author(s): Yuan, Y.R., Pei, Y., Ma, J.B., Kuryavyi, V., Zhadina, M., Meister, G., Chen, H.Y., Dauter, Z., Tuschl, T., Patel, D.J.

Revision History  

• Version 1.0: 2005-08-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance