1U04 | pdb_00001u04

Crystal structure of full length Argonaute from Pyrococcus furiosus

• PDB DOI: https://doi.org/10.2210/pdb1U04/pdb

• Classification: HYDROLASE/GENE REGULATION
• Organism(s): Pyrococcus furiosus DSM 3638
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-07-12 Released: 2004-08-17 
• Deposition Author(s): Song, J.J., Smith, S.K., Hannon, G.J., Joshua-Tor, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.258 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of Argonaute and its implications for RISC slicer activity.

Song, J.J., Smith, S.K., Hannon, G.J., Joshua-Tor, L.

(2004) Science 305: 1434-1437

• PubMed: 15284453 
• DOI: https://doi.org/10.1126/science.1102514
• Primary Citation Related Structures: 
  1U04


• PubMed Abstract: 
  

  Argonaute proteins and small interfering RNAs (siRNAs) are the known signature components of the RNA interference effector complex RNA-induced silencing complex (RISC). However, the identity of "Slicer," the enzyme that cleaves the messenger RNA (mRNA) as directed by the siRNA, has not been resolved. Here, we report the crystal structure of the Argonaute protein from Pyrococcus furiosus at 2.25 angstrom resolution. The structure reveals a crescent-shaped base made up of the amino-terminal, middle, and PIWI domains. The Piwi Argonaute Zwille (PAZ) domain is held above the base by a "stalk"-like region. The PIWI domain (named for the protein piwi) is similar to ribonuclease H, with a conserved active site aspartate-aspartate-glutamate motif, strongly implicating Argonaute as "Slicer." The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage.

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Organizational Affiliation: 
• Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.44 kDa 
• Atom Count: 6,112 
• Modeled Residue Count: 713 
• Deposited Residue Count: 771 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PF0537	A	771	Pyrococcus furiosus DSM 3638	Mutation(s): 1  EC: 3.1.24
UniProt
Find proteins for Q8U3D2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3D2  Go to UniProtKB:  Q8U3D2

Small Molecules

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: 2.25 Å
• R-Value Free:  0.258 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.726	α = 90
b = 104.188	β = 102.83
c = 74.015	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-17 
Deposition Author(s): Song, J.J., Smith, S.K., Hannon, G.J., Joshua-Tor, L.

Revision History  

• Version 1.0: 2004-08-17
  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
• Version 1.3: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary
• Version 1.5: 2026-02-11
  Changes: Data collection, Database references