4OLA | pdb_00004ola

Crystal Structure of Human Argonaute2

• PDB DOI: https://doi.org/10.2210/pdb4OLA/pdb
• Entry: 4OLA supersedes: 4EI1
• NAKB: 4OLA

• Classification: HYDROLASE/RNA
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-01-23 Released: 2014-02-05 
• Deposition Author(s): Schirle, N.T., MacRae, I.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

The crystal structure of human Argonaute2.

Schirle, N.T., MacRae, I.J.

(2012) Science 336: 1037-1040

• PubMed: 22539551 
• DOI: https://doi.org/10.1126/science.1221551
• Primary Citation Related Structures: 
  4OLA, 4OLB


• PubMed Abstract: 
  

  Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans.

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Organizational Affiliation: 
• Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, 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: 100.76 kDa 
• Atom Count: 6,722 
• Modeled Residue Count: 799 
• Deposited Residue Count: 869 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	A	859	Homo sapiens	Mutation(s): 1  Gene Names: EIF2C2, AGO2 EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV8 (Homo sapiens) Explore Q9UKV8  Go to UniProtKB:  Q9UKV8
PHAROS:  Q9UKV8 GTEx:  ENSG00000123908

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*U)-3'	B	10	Homo sapiens

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPH	C [auth A]	PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N
IPA	D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.157	α = 90
b = 107.669	β = 107.1
c = 68.522	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-05 
Deposition Author(s): Schirle, N.T., MacRae, I.J.
• This entry supersedes: 4EI1

Revision History  

• Version 1.0: 2014-02-05
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations