3QX9

Crystal structure of MID domain from hAGO2 in complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb3QX9/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-01 Released: 2011-04-20 
• Deposition Author(s): Frank, F., Fabian, M.R., Stepinski, J., Jemielity, J., Darzynkiewicz, E., Sonenberg, N., Nagar, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Structural analysis of 5'-mRNA-cap interactions with the human AGO2 MID domain.

Frank, F., Fabian, M.R., Stepinski, J., Jemielity, J., Darzynkiewicz, E., Sonenberg, N., Nagar, B.

(2011) EMBO Rep 12: 415-420

• PubMed: 21475248 
• DOI: https://doi.org/10.1038/embor.2011.48
• Primary Citation of Related Structures:  
  3QX8, 3QX9


• PubMed Abstract: 
  

  In RNA silencing, microRNA (miRNA)-mediated translational repression occurs through mechanisms that do not invoke messenger-RNA (mRNA) target cleavage by Argonaute proteins. The nature of these mechanisms is unclear, but several recent studies have proposed that a direct interaction between the mRNA-cap and the middle (MID) domain of Argonautes is involved. Here, we present crystallographic and NMR data demonstrating that cap analogues do not bind significantly to the isolated MID domain of human Argonaute 2 (hAGO2) and are found in the miRNA 5'-nucleotide binding site in an implausible binding mode. Additionally, in vitro pull-down experiments with full-length hAGO2 indicate that the interaction with cap analogues is nonspecific.

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Organizational Affiliation: 

Department of Biochemistry, McGill University, 1160 Pine Avenue West, Montreal, Quebec H3A 1A3, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.5 kDa 
• Atom Count: 3,429 
• Modelled Residue Count: 400 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	A, B, C	138	Homo sapiens	Mutation(s): 0  Gene Names: EIF2C2, AGO2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV8 (Homo sapiens) Explore Q9UKV8  Go to UniProtKB:  Q9UKV8
PHAROS:  Q9UKV8 GTEx:  ENSG00000123908

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], E [auth B], F [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ATP	PDBBind:  3QX9	Kd: 9.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.494	α = 87.14
b = 46.508	β = 73.56
c = 65.817	γ = 84.56

Software Package:

Software Name	Purpose
HKL-2000	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: 2011-04-20 
Deposition Author(s): Frank, F., Fabian, M.R., Stepinski, J., Jemielity, J., Darzynkiewicz, E., Sonenberg, N., Nagar, B.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-29
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations