5AWH

Rhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex

• PDB DOI:  https://doi.org/10.2210/pdb5AWH/pdb
• NAKB: 5AWH

• Classification: RNA BINDING PROTEIN/DNA/RNA
• Organism(s): Cereibacter sphaeroides ATCC 17025, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-03 Released: 2016-07-06 
• Deposition Author(s): Miyoshi, T., Ito, K., Murakami, R., Uchiumi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.

Miyoshi, T., Ito, K., Murakami, R., Uchiumi, T.

(2016) Nat Commun 7: 11846-11846

• PubMed: 27325485 
• DOI: https://doi.org/10.1038/ncomms11846
• Primary Citation of Related Structures:  
  5AWH


• PubMed Abstract: 
  

Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson-Crick base-pairing even in the 3'-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5' base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region.

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Organizational Affiliation: 

Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan.

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)

Macromolecule Content

• Total Structure Weight: 196.83 kDa 
• Atom Count: 13,805 
• Modelled Residue Count: 1,546 
• Deposited Residue Count: 1,628 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	778	Cereibacter sphaeroides ATCC 17025	Mutation(s): 0  Gene Names: Rsph17025_3694
UniProt
Find proteins for A4WYU7 (Cereibacter sphaeroides (strain ATCC 17025 / ATH 2.4.3)) Explore A4WYU7  Go to UniProtKB:  A4WYU7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3')	C, E	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3')	D, F	18	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth C], H [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.186	α = 90
b = 118.303	β = 95.83
c = 118.48	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SHARP	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Miyoshi, T., Ito, K., Murakami, R., Uchiumi, T.

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Derived calculations