3MJ0 | pdb_00003mj0

Crystal Structure of Drosophia Ago-PAZ domain in complex with 3'-end 2'-O-methylated RNA

• PDB DOI: https://doi.org/10.2210/pdb3MJ0/pdb
• NAKB: 3MJ0

• Classification: RNA/RNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-04-12 Released: 2011-05-25 
• Deposition Author(s): Huang, Y., Ding, L., Ma, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.274 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of drosophila Ago2 PAZ domain in complex with 3'-end 2'-O-methylated RNA

Huang, Y., Ding, L., Ma, J.

To be published.

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: 16.98 kDa 
• Atom Count: 1,170 
• Modeled Residue Count: 127 
• Deposited Residue Count: 133 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute-2	A	124	Drosophila melanogaster	Mutation(s): 0  Gene Names: AGO2, CG7439
UniProt
Find proteins for Q9VUQ5 (Drosophila melanogaster) Explore Q9VUQ5  Go to UniProtKB:  Q9VUQ5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*GP*UP*UP*AP*CP*GP*CP*(OMU))-3')	B	9	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.274 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.211	α = 90
b = 116.796	β = 90
c = 38.661	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Huang, Y., Ding, L., Ma, J.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description