4KRE | pdb_00004kre

Structure of Human Argonaute-1 bound to endogenous Sf9 RNA

• PDB DOI: https://doi.org/10.2210/pdb4KRE/pdb
• NAKB: 4KRE

• Classification: TRANSCRIPTION/RNA
• Organism(s): Homo sapiens, Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2013-05-16 Released: 2013-06-19 
• Deposition Author(s): Faehnle, C.R., Elkayam, E., Joshua-Tor, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

The making of a slicer: activation of human argonaute-1.

Faehnle, C.R., Elkayam, E., Haase, A.D., Hannon, G.J., Joshua-Tor, L.

(2013) Cell Rep 3: 1901-1909

• PubMed: 23746446 
• DOI: https://doi.org/10.1016/j.celrep.2013.05.033
• Primary Citation Related Structures: 
  4KRE, 4KRF


• PubMed Abstract: 
  

  Argonautes are the central protein component in small RNA silencing pathways. Of the four human Argonautes (hAgo1-hAgo4) only hAgo2 is an active slicer. We determined the structure of hAgo1 bound to endogenous copurified RNAs to 1.75 Å resolution and hAgo1 loaded with let-7 microRNA to 2.1 Å. Both structures are strikingly similar to the structures of hAgo2. A conserved catalytic tetrad within the PIWI domain of hAgo2 is required for its slicing activity. Completion of the tetrad, combined with a mutation on a loop adjacent to the active site of hAgo1, results in slicer activity that is substantially enhanced by swapping in the N domain of hAgo2. hAgo3, with an intact tetrad, becomes an active slicer by swapping the N domain of hAgo2 without additional mutations. Intriguingly, the elements that make Argonaute an active slicer involve a sophisticated interplay between the active site and more distant regions of the enzyme.

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Organizational Affiliation: 
• W.M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103.89 kDa 
• Atom Count: 7,179 
• Modeled Residue Count: 810 
• Deposited Residue Count: 878 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-1	A	858	Homo sapiens	Mutation(s): 0  Gene Names: AGO1, EIF2C1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL18 (Homo sapiens) Explore Q9UL18  Go to UniProtKB:  Q9UL18
PHAROS:  Q9UL18 GTEx:  ENSG00000092847

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*UP*AP*UP*UP*AP*AP*A*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')	B [auth R]	20	Spodoptera frugiperda

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.47	α = 90
b = 98.63	β = 110.96
c = 73.21	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Faehnle, C.R., Elkayam, E., Joshua-Tor, L.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references