6D9K | pdb_00006d9k

Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-G Non-canonical Pair

• PDB DOI: https://doi.org/10.2210/pdb6D9K/pdb
• NAKB: 6D9K

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


• Deposited: 2018-04-30 Released: 2018-07-25 
• Deposition Author(s): Liu, Y., Esyunina, D., Olovnikov, I., Teplova, M., Patel, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.

Liu, Y., Esyunina, D., Olovnikov, I., Teplova, M., Kulbachinskiy, A., Aravin, A.A., Patel, D.J.

(2018) Cell Rep 24: 453-462

• PubMed: 29996105 
• DOI: https://doi.org/10.1016/j.celrep.2018.06.021
• Primary Citation Related Structures: 
  6D8A, 6D8F, 6D8P, 6D92, 6D95, 6D9K, 6D9L


• PubMed Abstract: 
  

  Prokaryotic Argonaute (Ago) proteins were recently shown to target foreign genetic elements, thus making them a perfect model for studies of interference mechanisms. Here, we study interactions of Rhodobacter sphaeroides Ago (RsAgo) with guide RNA (gRNA) and fully complementary or imperfect target DNA (tDNA) using biochemical and structural approaches. We show that RsAgo can specifically recognize both the first nucleotide in gRNA and complementary nucleotide in tDNA, and both interactions contribute to nucleic acid binding. Non-canonical pairs and bulges on the target strand can be accommodated by RsAgo with minimal perturbation of the duplex but significantly reduce RsAgo affinity to tDNA. Surprisingly, mismatches between gRNA and tDNA induce dissociation of the guide-target duplex from RsAgo. Our results reveal plasticity in the ability of Ago proteins to accommodate helical imperfections, show how this might affect the efficiency of RNA silencing, and suggest a potential mechanism for guide release and Ago recycling.

---

Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia. Electronic address: [e-mail].
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address: [e-mail].
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address: [e-mail].

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: 204.81 kDa 
• Atom Count: 13,456 
• Modeled Residue Count: 1,589 
• Deposited Residue Count: 1,666 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, D [auth F]	791	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'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')	B [auth C], E [auth H]	18	Cereibacter sphaeroides ATCC 17025

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*GP*GP*CP*AP*GP*TP*AP*AP*C)-3')	C [auth G], F [auth J]	24	Cereibacter sphaeroides ATCC 17025

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	H [auth A], M [auth H]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	G [auth A], J [auth F], K [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	I [auth C], L [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.119	α = 90
b = 119.13	β = 95.6
c = 118.134	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Liu, Y., Esyunina, D., Olovnikov, I., Teplova, M., Patel, D.J.

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations